Combined transcriptomics and proteomics analysis of Perk toxicity pathways

General information

This pipeline relates to data included in Figures 2 to 7, as well as in supplementary tables, part of the supplementary materials, from our study titled Combined transcriptomics and proteomics analysis of Perk toxicity pathways,
by Rebeka Popovic, Ivana Celardo, Yizhou Yu, Ana C. Costa, Samantha H. Y. Loh and L. Miguel Martins at the MRC Toxicology Unit, University of Cambridge.

Aims and objectives

AIM: Analyse transcriptomics and proteomics data from UASdPERK overexpressing flies:

1) Define targets: Compare mRNA and protein upregulation/downregulation, obtain gene lists (R/R Studio)

2) Perform upstream analysis on the obtained gene list (iRegulon)

3) Perform pathway enrichment analysis on the obtained lists (ClueGO)

Experimental background

Genotypes:

• tubgal80,daGal4>+
• tubgal80,daGal4>UASPERK

Transcriptomics: Crosses were kept at 18C and moved to 29C for 15h following eclosion, 4 biological replicates were used. RNA was extracted using the TRIZOL method and analysed by microarray analysis.

Proteomics: Crosses were kept at 18C and moved to 29C for 15h following eclosion, males, 5 biological replicates were used. The samples were frozen after collection, the protein extraction was performed with RIPA, and analysed by Tandem Mass Tagging (TMT) proteomics analysis.

Define targets

The chosen FC value is 1.6 (or for logged values 0.7).

Load packages and preprocess data

library(tidyverse)

## Warning: package 'tidyverse' was built under R version 3.5.2

## Warning: package 'tidyr' was built under R version 3.5.2

## Warning: package 'purrr' was built under R version 3.5.2

## Warning: package 'stringr' was built under R version 3.5.2

## Warning: package 'forcats' was built under R version 3.5.2

library(kableExtra)
library(ggthemes)

## Warning: package 'ggthemes' was built under R version 3.5.2

library(scales)
# install.packages("ggpubr")
library(ggpubr)
theme_set(theme_pubr())
library(ggrepel)

## Warning: package 'ggrepel' was built under R version 3.5.2

# Load dataset with inner joined dPERK transcripts and proteins (matched only) # Supplementary Table 12
dPERK_inner_join <- read.delim("1.6_data/dPERK_inner_join.csv",  header = TRUE, sep = ",") 

# Define thresholds for transcripts: FC=1.6 and FDR=0.05 
dPERK_inner_join$trans_reg <- ifelse(dPERK_inner_join$trans_FC >= 1.6 & dPERK_inner_join$trans_FDR <= 0.05, 1, ifelse(dPERK_inner_join$trans_FC <= -1.6 & dPERK_inner_join$trans_FDR <= 0.05, -1, 0))

# Define thresholds for proteins: FC=0.7 (the values are loged) and FDR=0.05 
dPERK_inner_join$prot_reg <- ifelse(dPERK_inner_join$prot_FC >= 0.7 & dPERK_inner_join$prot_FDR <= 0.05, 1, ifelse(dPERK_inner_join$prot_FC <= -0.7 & dPERK_inner_join$prot_FDR <= 0.05, -1, 0))

# Save
write.csv(dPERK_inner_join, "1.6_data_output/dPERK_inner_join_FC1.6.csv")


# Load the dataset with all transcripts (not all matched to proteins)  # Supplementary Table 1
dPERK_full_join <- read.delim("1.6_data/dPERK_full_join.csv",  header = TRUE, sep = ",") 

# Define thresholds for transcripts and proteins  
dPERK_full_join$trans_reg <- ifelse(dPERK_full_join$trans_FC >= 1.6 & dPERK_full_join$trans_FDR <= 0.05, 1, ifelse(dPERK_full_join$trans_FC <= -1.6 & dPERK_full_join$trans_FDR <= 0.05, -1, 0))
dPERK_full_join$prot_reg <- ifelse(dPERK_full_join$prot_FC >= 0.7 & dPERK_full_join$prot_FDR <= 0.05, 1, ifelse(dPERK_full_join$prot_FC <= -0.7 & dPERK_full_join$prot_FDR <= 0.05, -1, 0))

write.csv(dPERK_full_join, "1.6_data_output/dPERK_full_join_FC1.6.csv")


# no of unique proteins
count_proteomics <- dPERK_inner_join$Protein.ID %>% unique() # 5,739
count_gene <- dPERK_inner_join$Gene.name %>% unique() # 5,586

# no of unique transcripts 
count_transcriptomics <- dPERK_full_join$Transcript.ID %>% unique() #32,503

# no of unique genes, based on all transcripts 
dPERK_full_join_unique_genes2 <- dPERK_full_join  %>% select(Gene.name) %>% unique() # 15,635 

Visualise groups: MS plot DEA (equal scale)

This figure is related to Figure 4.

yy <- dPERK_inner_join # creating another object to avoid changing original data

# Transforming the transcriptomics values so they can be logged and more equally represented

# The data was transformed previously by the person who processed this data via inverse or reciprocal transformation, meaning all the FCvalue < 1 were -1/FCvalue. Whilst this does convert the expression ratio into a fold change, the problem with this method is that the mapping space is discontinuous between -1 and 1 & hence becomes a problem for most mathematical steps downstream of this step...

# Convert the values that have been transformed in trans_FC in this inner join dataset too, so I can log2 transform them 
yy$trans_FC_true = case_when (yy$trans_FC <= 0 ~ -1/yy$trans_FC, TRUE ~ as.numeric(yy$trans_FC))

# Define different subgroups 
yy$ind <- "Not regulated"
for (i in 1:dim(yy)[1]){
  if (yy$prot_reg[i] > 0 & yy$trans_reg[i] == 0) {
    yy$ind[i] <- "Up in proteomics, no change in transcriptomics"
  }
  if (yy$prot_reg[i] < 0 & yy$trans_reg[i] == 0) {
    yy$ind[i] <- "Down in proteomics, no change in transcriptomics"
  }
  if (yy$trans_reg[i] > 0 & yy$prot_reg[i] == 0) {
    yy$ind[i] <- "Up in transcriptomics, no change in proteomics"
  }
  if (yy$trans_reg[i] < 0 & yy$prot_reg[i] == 0) {
    yy$ind[i] <- "Down in transcriptomics, no change in proteomics"
  }
  if (yy$prot_reg[i] > 0 & yy$trans_reg[i] > 0) {
    yy$ind[i] <- "Up in proteomics and transcriptomics"
  }
  if (yy$prot_reg[i] < 0 & yy$trans_reg[i] < 0) {
    yy$ind[i] <- "Down in proteomics and transcriptomics"
  }
  if (yy$prot_reg[i] > 0 & yy$trans_reg[i] < 0) {
    yy$ind[i] <- "Up in proteomics and down in transcriptomics"
  }
  if (yy$prot_reg[i] < 0 & yy$trans_reg[i] > 0) {
    yy$ind[i] <- "Down in proteomics and up in transcriptomics"
  }
  if (yy$prot_reg[i] > 0 & yy$trans_reg[i] < 0) {
    yy$ind[i] <- "Up in proteomics and down in transcriptomics"
  }
}

 #yy <- yy %>% arrange((ind))

yy_transFDR = subset(yy, trans_FDR <= 0.05)
yy_bothFDR = subset(yy_transFDR, prot_FDR <= 0.05)

# PERK label  
yy_bothFDR$genelabels <- ""
yy_bothFDR$genelabels <- ifelse(yy_bothFDR$Gene.name == "PEK", TRUE,FALSE)

# Plot
ggplot(yy_bothFDR, aes(x = log2(trans_FC_true), y = prot_FC)) + 
  geom_point(data = yy_bothFDR, size = 1, alpha = 0.6, aes(colour = factor(ind))) +
  geom_smooth(method = "lm")+
  
  geom_vline(xintercept = log2(1.6), colour="#990000", linetype="dashed") + 
  geom_vline(xintercept = -log2(1.6), colour="#990000", linetype="dashed") + 
  geom_hline(yintercept = log2(1.6), colour="#990000", linetype="dashed") + 
  geom_hline(yintercept = -log2(1.6), colour="#990000", linetype="dashed") + 
  
  theme_classic(base_size = 14) + 
  ylab(expression(log[2]("Proteome FC"))) + 
  xlab(expression(log[2]("Transcriptome FC"))) + coord_cartesian(xlim = c(-8, 8), ylim = c(-8, 8)) + 
  #theme(legend.position = "none") + 
  scale_y_continuous(breaks=seq(-8,8,2)) + scale_x_continuous(breaks=seq(-8,8,2)) + scale_colour_tableau(name = "") + guides(colour = guide_legend(override.aes = list(size=2))) +
  geom_text_repel(aes(x = log2(trans_FC_true), y = prot_FC, label = ifelse(genelabels == TRUE, as.character(Gene.name),""))) + theme(legend.title = element_text(size = 6), legend.text = element_text(size = 6))

## `geom_smooth()` using formula 'y ~ x'

ggsave("1.6_figure_output/MA_transformed1.6_2_yy.pdf", scale = 1, limitsize = TRUE, width = 11, height = 6)

## `geom_smooth()` using formula 'y ~ x'

# Correlation 
cor.test(log2(yy_bothFDR$trans_FC_true),yy_bothFDR$prot_FC)

## 
##  Pearson's product-moment correlation
## 
## data:  log2(yy_bothFDR$trans_FC_true) and yy_bothFDR$prot_FC
## t = 32.631, df = 3140, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
##  0.4766447 0.5288871
## sample estimates:
##       cor 
## 0.5032256

Gene lists

1) Upregulated transcripts

Count: 977 transcripts, 517 genes

This table is related to Supplementary Table 2.

# Filter rows which have FC bigger or equal to 1.6 and FDR value smaller or equal to 0.05, as predefined earlier 
TUP_full_FC1.6 <- dPERK_full_join %>% filter (trans_reg == 1)
# Create another list without duplicates 
TUP_full_FC1.6_unq <- TUP_full_FC1.6  %>% dplyr::select(Gene.name) %>%  unique()
write.csv(TUP_full_FC1.6, "1.6_data_output/TUP_full_FC1.6.csv")
write.csv(TUP_full_FC1.6_unq, "1.6_data_output/TUP_full_FC1.6_unq.csv")

Table 1: Upregulated transcripts

Transcript ID	Gene ID	Transcript FC
FBtr0073252	Cpr64Ac	119.00
FBtr0087451	Cyp6a17	117.00
FBtr0345527	Cyp6a17	117.00
FBtr0088591	Cyp4p2	115.00
FBtr0100559	Hsp22	74.60
FBtr0078596	Osi6	74.30
FBtr0346344	Osi6	74.30
FBtr0077958	MFS3	70.50
FBtr0302379	CG5999	69.40
FBtr0100655	Hsp67Bb	29.20
FBtr0100558	Hsp22	29.20
FBtr0113169	CG12520	27.80
FBtr0343628	CG12520	27.80
FBtr0086774	Dgp-1	25.80
FBtr0086773	Dgp-1	21.20
FBtr0082657	CG5724	21.00
FBtr0330026	PEK	16.90
FBtr0330027	PEK	16.90
FBtr0078770	PEK	16.60
FBtr0077008	ImpL3	16.30
FBtr0332066	ImpL3	16.20
FBtr0332067	ImpL3	16.10
FBtr0332065	ImpL3	16.00
FBtr0334132	CG44006	13.10
FBtr0332623	CG12057	9.59
FBtr0071304	CG12057	9.41
FBtr0084870	CG10420	8.58
FBtr0091787	CG33786	8.08
FBtr0091786	CG33785	8.08
FBtr0343000	CG4269	8.01
FBtr0306924	CG43320	7.85
FBtr0071854	CG4269	7.77
FBtr0343001	CG4269	7.73
FBtr0289990	CG30022	7.58
FBtr0082569	GstD2	7.49
FBtr0086749	CG10916	7.12
FBtr0273384	CG8213	7.10
FBtr0273385	CG8213	7.10
FBtr0339307	CG8213	7.10
FBtr0332853	CG10916	7.09
FBtr0089055	Cyp9b2	6.96
FBtr0078098	CG11911	6.96
FBtr0343842	CG43402	6.77
FBtr0308745	CG43402	6.77
FBtr0085210	CG5646	6.11
FBtr0089049	Gadd45	5.89
FBtr0345581	CG3264	5.84
FBtr0071781	CG3264	5.84
FBtr0079299	Aatf	5.73
FBtr0331433	CG10778	5.41
FBtr0340400	cactin	5.39
FBtr0082334	Tpc1	5.36
FBtr0336761	Nmdmc	5.34
FBtr0081996	Nmdmc	5.33
FBtr0301935	Sfp26Ad	5.32
FBtr0333233	Sfp26Ad	5.32
FBtr0086133	Cyp6a2	5.32
FBtr0082333	Tpc1	5.30
FBtr0071131	CG10778	5.01
FBtr0339391	Aats-asp	4.91
FBtr0342608	JhI-21	4.87
FBtr0344927	CR45141	4.87
FBtr0300233	Uhg8	4.84
FBtr0074730	CG14205	4.84
FBtr0305089	JhI-21	4.83
FBtr0087784	Aats-asp	4.83
FBtr0332882	Aats-asp	4.82
FBtr0087735	Aats-val	4.81
FBtr0089656	JhI-21	4.80
FBtr0089655	JhI-21	4.78
FBtr0346427	JhI-21	4.76
FBtr0087734	Aats-val	4.75
FBtr0333148	Aats-val	4.75
FBtr0081997	Nmdmc	4.74
FBtr0084035	CG7044	4.65
FBtr0085849	FeCH	4.60
FBtr0085850	FeCH	4.58
FBtr0080912	Ugt36Bc	4.58
FBtr0080911	Ugt36Bc	4.58
FBtr0085851	FeCH	4.57
FBtr0344850	Ugt36Bc	4.53
FBtr0347325	CR46092	4.47
FBtr0100353	ade3	4.45
FBtr0075665	CG12310	4.44
FBtr0342974	wus	4.35
FBtr0074418	wus	4.35
FBtr0078066	CG2789	4.35
FBtr0089463	asparagine-synthetase	4.30
FBtr0079253	CG9505	4.28
FBtr0077721	daw	4.28
FBtr0077720	daw	4.26
FBtr0335151	daw	4.26
FBtr0084511	Aats-glupro	4.24
FBtr0273217	CG17751	4.23
FBtr0086828	POSH	4.22
FBtr0075120	rpr	4.20
FBtr0089056	Cyp9b1	4.19
FBtr0089419	Cyp12d1-p	4.13
FBtr0073729	CG32641	4.12
FBtr0079442	CG15818	4.12
FBtr0086325	CG16898	4.11
FBtr0303763	rempA	4.07
FBtr0074739	Shawn	4.01
FBtr0334308	Irbp	3.98
FBtr0081981	Aats-trp	3.97
FBtr0081953	CG9773	3.96
FBtr0080288	Qtzl	3.96
FBtr0074979	CG9451	3.94
FBtr0333845	CG9451	3.94
FBtr0087547	Arc2	3.92
FBtr0339524	Qtzl	3.89
FBtr0344263	GstD9	3.87
FBtr0082608	GstD9	3.87
FBtr0073061	Drsl4	3.87
FBtr0078235	trbl	3.86
FBtr0301717	CG42588	3.85
FBtr0082385	Irbp	3.84
FBtr0084047	CG17278	3.82
FBtr0078500	Aats-ile	3.80
FBtr0078499	Aats-ile	3.80
FBtr0078498	Aats-ile	3.79
FBtr0345800	CG12164	3.79
FBtr0088963	CG12164	3.79
FBtr0345640	CG33123	3.77
FBtr0077562	CG33123	3.77
FBtr0301144	CG5953	3.77
FBtr0079486	Uro	3.73
FBtr0304053	CG42588	3.72
FBtr0089418	Cyp12d1-d	3.72
FBtr0334282	Rgk1	3.71
FBtr0334284	Rgk1	3.71
FBtr0084828	CG13659	3.71
FBtr0080615	NimC1	3.67
FBtr0074736	Tyler	3.66
FBtr0074737	Shawn	3.66
FBtr0332909	asrij	3.66
FBtr0079431	ade3	3.66
FBtr0339663	ade3	3.66
FBtr0346617	Tyler	3.65
FBtr0074738	Shawn	3.65
FBtr0346616	Tyler	3.65
FBtr0344069	Shawn	3.65
FBtr0321281	CG7632	3.63
FBtr0086842	Uhg1	3.61
FBtr0333558	Uhg1	3.61
FBtr0344740	Skp2	3.61
FBtr0078339	CG7632	3.57
FBtr0071902	asrij	3.54
FBtr0344998	CG44004	3.53
FBtr0344997	CG44004	3.53
FBtr0086912	l(2)k01209	3.52
FBtr0113321	Ugt86Dd	3.48
FBtr0070272	b6	3.43
FBtr0081095	CG10336	3.43
FBtr0084512	Aats-glupro	3.42
FBtr0086913	l(2)k01209	3.39
FBtr0086914	l(2)k01209	3.39
FBtr0080402	CG15483	3.39
FBtr0111206	CG14636	3.38
FBtr0078988	CG14636	3.38
FBtr0086915	l(2)k01209	3.36
FBtr0074593	Aats-his	3.36
FBtr0333805	Aats-his	3.34
FBtr0070777	CG15784	3.34
FBtr0302360	Lectin-galC1	3.34
FBtr0075904	CG32115	3.33
FBtr0340460	CG15784	3.33
FBtr0333804	Aats-his	3.32
FBtr0273194	CG10336	3.31
FBtr0302027	Mrp4	3.29
FBtr0086813	CG5773	3.28
FBtr0345472	CG5773	3.28
FBtr0340281	CG5773	3.28
FBtr0333806	Aats-his	3.26
FBtr0302331	Cyp6a14	3.26
FBtr0081201	Lectin-galC1	3.26
FBtr0310075	NimC1	3.24
FBtr0343644	NimC1	3.24
FBtr0072013	eIF2B-delta	3.23
FBtr0290232	InR	3.22
FBtr0290231	InR	3.22
FBtr0079925	Cyp4e3	3.22
FBtr0082438	CG6834	3.21
FBtr0084121	InR	3.21
FBtr0345575	Cyp6a14	3.20
FBtr0290230	InR	3.20
FBtr0086675	GstE7	3.19
FBtr0079722	Aats-ala	3.18
FBtr0302315	eIF2B-delta	3.18
FBtr0072014	eIF2B-delta	3.16
FBtr0087677	CG13334	3.16
FBtr0081162	Aats-asn	3.13
FBtr0079721	Aats-ala	3.12
FBtr0306923	CG43319	3.12
FBtr0332578	Aats-asn	3.11
FBtr0304877	CG43095	3.09
FBtr0073520	CG1703	3.09
FBtr0343647	CG1703	3.09
FBtr0333357	Pbgs	3.08
FBtr0076011	Pbgs	3.08
FBtr0073777	CG1673	3.08
FBtr0083792	tRNA:V3b:92Bb	3.07
FBtr0073249	ImpL2	3.07
FBtr0333569	ImpL2	3.07
FBtr0072015	eIF2B-delta	3.06
FBtr0076457	aay	3.06
FBtr0073172	CG12766	3.05
FBtr0083354	CG14907	3.05
FBtr0087139	JhI-26	3.02
FBtr0331609	CG10802	3.02
FBtr0076894	CG14820	3.02
FBtr0081276	CG10337	3.02
FBtr0340614	Ranbp21	3.01
FBtr0082420	Elp1	3.01
FBtr0335447	Elp1	3.01
FBtr0335448	Elp1	3.01
FBtr0074759	Ranbp21	3.00
FBtr0113093	CG10924	3.00
FBtr0071326	c11.1	2.98
FBtr0343368	c11.1	2.98
FBtr0085172	CG3348	2.97
FBtr0070568	CG10802	2.96
FBtr0073250	ImpL2	2.95
FBtr0082600	lig3	2.95
FBtr0073248	ImpL2	2.94
FBtr0305955	CG13334	2.92
FBtr0303475	Fdxh	2.91
FBtr0076498	Fdxh	2.91
FBtr0088360	JhI-1	2.90
FBtr0079891	CG5846	2.90
FBtr0346717	CG5846	2.90
FBtr0345628	GstE11	2.90
FBtr0086697	GstE11	2.90
FBtr0339359	slbo	2.90
FBtr0078099	CG11912	2.90
FBtr0077547	CG16713	2.87
FBtr0335480	CG17259	2.87
FBtr0077667	CG17259	2.87
FBtr0072272	slbo	2.87
FBtr0305607	CG43155	2.87
FBtr0082570	GstD3	2.86
FBtr0077165	CG4611	2.84
FBtr0078226	CG11796	2.82
FBtr0078225	CG11796	2.81
FBtr0086855	snoRNA:U31:54Ed	2.81
FBtr0070283	CG3740	2.79
FBtr0078663	CG2017	2.78
FBtr0345440	CR43358	2.78
FBtr0307108	CR43358	2.78
FBtr0086911	Prosalpha5	2.75
FBtr0300127	Cyp6a20	2.74
FBtr0345939	CG42362	2.74
FBtr0345940	CG42363	2.74
FBtr0299962	CG42363	2.74
FBtr0299961	CG42362	2.74
FBtr0084913	CG14545	2.73
FBtr0088834	CG1882	2.73
FBtr0345697	CG1882	2.73
FBtr0339120	CG1882	2.73
FBtr0070625	CG6428	2.72
FBtr0087121	CG8311	2.71
FBtr0333962	RhoGEF3	2.70
FBtr0086676	GstE8	2.70
FBtr0345798	GstE8	2.70
FBtr0082338	Ugt86Da	2.69
FBtr0345543	CG31955	2.69
FBtr0087684	CG33156	2.69
FBtr0339606	DNApol-iota	2.67
FBtr0077540	CG31955	2.67
FBtr0345639	CG31955	2.67
FBtr0088836	CG1882	2.66
FBtr0335167	Cyp309a1	2.66
FBtr0335166	Cyp309a1	2.66
FBtr0333961	RhoGEF3	2.65
FBtr0080587	Cyp28a5	2.65
FBtr0332960	CG2004	2.65
FBtr0339598	tx	2.63
FBtr0085009	tx	2.63
FBtr0086699	CG10924	2.63
FBtr0081797	DNApol-iota	2.62
FBtr0081729	Neurochondrin	2.62
FBtr0089643	CG11710	2.62
FBtr0089642	CG11710	2.62
FBtr0339682	CG11710	2.62
FBtr0075159	CG5535	2.61
FBtr0273277	CG5535	2.61
FBtr0078661	CG2017	2.60
FBtr0114518	CG2017	2.60
FBtr0078664	CG2017	2.60
FBtr0078662	CG2017	2.60
FBtr0113450	CG33156	2.59
FBtr0087683	CG33156	2.58
FBtr0075968	eIF-2beta	2.57
FBtr0081798	DNApol-iota	2.56
FBtr0347257	CG5791	2.56
FBtr0084180	CG5791	2.56
FBtr0070714	Proc-R	2.55
FBtr0080333	Aats-thr	2.55
FBtr0088564	Dbp45A	2.54
FBtr0088928	CG1942	2.54
FBtr0332957	CG2004	2.53
FBtr0346167	CG2004	2.53
FBtr0332958	CG2004	2.53
FBtr0071281	CG2004	2.53
FBtr0335196	CG5791	2.53
FBtr0070713	Proc-R	2.52
FBtr0345320	Proc-R	2.52
FBtr0077306	mal	2.52
FBtr0100551	Proc-R	2.51
FBtr0100552	Proc-R	2.51
FBtr0089941	scf	2.50
FBtr0344987	mal	2.50
FBtr0345350	CG10638	2.50
FBtr0089321	CG10638	2.50
FBtr0075632	Aats-gly	2.49
FBtr0333934	Aats-gly	2.49
FBtr0088835	CG1882	2.49
FBtr0331342	CD98hc	2.48
FBtr0332157	CD98hc	2.48
FBtr0081824	CD98hc	2.48
FBtr0331344	CD98hc	2.48
FBtr0337091	CG5953	2.48
FBtr0080873	CG5953	2.48
FBtr0089942	scf	2.47
FBtr0080914	CG13272	2.47
FBtr0345053	CR45176	2.47
FBtr0346428	l(2)37Cc	2.46
FBtr0081164	l(2)37Cc	2.46
FBtr0075633	Aats-gly	2.46
FBtr0300251	Uhg5	2.46
FBtr0343672	CG33307	2.46
FBtr0080565	CG33307	2.46
FBtr0336814	CG44194	2.46
FBtr0082721	CG17327	2.46
FBtr0345503	CG3746	2.46
FBtr0071929	CG3746	2.46
FBtr0081165	l(2)37Cc	2.43
FBtr0080331	Aats-thr	2.43
FBtr0073264	RfC4	2.43
FBtr0112724	CG34423	2.43
FBtr0344419	CG45061	2.43
FBtr0088837	CG1882	2.42
FBtr0339119	CG1882	2.42
FBtr0302518	CG13793	2.42
FBtr0346436	Aats-thr	2.41
FBtr0080332	Aats-thr	2.41
FBtr0073105	CG32271	2.41
FBtr0079389	CG3476	2.41
FBtr0299617	CG42272	2.40
FBtr0301854	CG34423	2.40
FBtr0080892	ChLD3	2.39
FBtr0300231	Uhg5	2.38
FBtr0088838	phr	2.37
FBtr0087452	Cyp6a23	2.37
FBtr0080874	CG5953	2.37
FBtr0339979	CG33469	2.36
FBtr0113458	CG33282	2.36
FBtr0088980	az2	2.35
FBtr0343971	CR43730	2.35
FBtr0070146	Rbf	2.34
FBtr0333952	RhoGEF3	2.34
FBtr0342583	CG31870	2.34
FBtr0087504	CG33469	2.34
FBtr0084216	CG18596	2.34
FBtr0080138	CG31870	2.33
FBtr0342584	CG31870	2.33
FBtr0080137	CG31870	2.33
FBtr0339924	CG40002	2.33
FBtr0344448	CG44194	2.32
FBtr0336813	CG17327	2.32
FBtr0086627	CG15100	2.31
FBtr0086674	GstE6	2.30
FBtr0336735	CR44168	2.30
FBtr0076946	Prat2	2.30
FBtr0078101	galectin	2.29
FBtr0339167	CG7720	2.29
FBtr0332459	NTPase	2.28
FBtr0112379	Rpb12	2.28
FBtr0343642	NimA	2.28
FBtr0344056	CR44990	2.28
FBtr0332460	NTPase	2.27
FBtr0333956	RhoGEF3	2.27
FBtr0300625	CG42496	2.27
FBtr0071672	Ppcdc	2.27
FBtr0342959	Ppcdc	2.27
FBtr0342958	CG42496	2.27
FBtr0331621	CG13272	2.27
FBtr0304720	NimA	2.27
FBtr0304719	NimA	2.27
FBtr0088839	phr	2.27
FBtr0074794	Alr	2.26
FBtr0299616	CG42272	2.26
FBtr0336486	CG14906	2.26
FBtr0331680	galectin	2.25
FBtr0336848	CG17107	2.25
FBtr0336847	CG17107	2.25
FBtr0080107	CG17107	2.25
FBtr0088494	CG1648	2.25
FBtr0077682	NTPase	2.24
FBtr0077683	NTPase	2.24
FBtr0077680	NTPase	2.24
FBtr0301200	CG7720	2.24
FBtr0301199	CG7720	2.24
FBtr0083678	CG7720	2.24
FBtr0343706	CG15282	2.23
FBtr0302946	CG15282	2.23
FBtr0078218	CG5059	2.23
FBtr0077389	CG3008	2.23
FBtr0089573	CG6686	2.22
FBtr0089572	CG6686	2.22
FBtr0301171	CG6686	2.22
FBtr0302164	galectin	2.22
FBtr0331567	CG5059	2.22
FBtr0300460	CG31909	2.22
FBtr0078219	CG5059	2.20
FBtr0078217	CG5059	2.20
FBtr0084405	CG31457	2.19
FBtr0100537	bocksbeutel	2.19
FBtr0113214	CG12945	2.18
FBtr0334685	CG12945	2.18
FBtr0308094	Mp	2.18
FBtr0081138	CG31793	2.18
FBtr0083679	CG7720	2.18
FBtr0078216	CG5059	2.17
FBtr0301735	CG12868	2.17
FBtr0086669	GstE1	2.17
FBtr0344942	f	2.16
FBtr0344220	CG32280	2.16
FBtr0073031	CG32280	2.16
FBtr0073030	CG32280	2.16
FBtr0300561	Atg1	2.16
FBtr0340318	CG31793	2.16
FBtr0305960	dia	2.16
FBtr0301201	CG7720	2.16
FBtr0073032	CG32280	2.15
FBtr0100669	CG14457	2.15
FBtr0331774	CG14457	2.15
FBtr0075945	Atg1	2.15
FBtr0070350	eIF2B-epsilon	2.15
FBtr0077524	Thor	2.15
FBtr0345289	Thor	2.15
FBtr0339974	CG42402	2.14
FBtr0081693	Ccp84Ac	2.14
FBtr0086214	GNBP-like3	2.14
FBtr0333958	RhoGEF3	2.13
FBtr0088831	mus205	2.13
FBtr0080547	CenG1A	2.13
FBtr0070351	eIF2B-epsilon	2.13
FBtr0080548	CenG1A	2.12
FBtr0086706	CG5323	2.12
FBtr0085456	CG15506	2.11
FBtr0082105	bocksbeutel	2.11
FBtr0087450	Cyp6a22	2.11
FBtr0345526	Cyp6a22	2.11
FBtr0339983	Cyp6a22	2.11
FBtr0110796	CG13624	2.10
FBtr0084674	CG13624	2.10
FBtr0084673	CG13624	2.10
FBtr0084054	ETHR	2.10
FBtr0334869	Orct2	2.10
FBtr0084598	Orct2	2.10
FBtr0112863	Phb2	2.09
FBtr0086615	Phb2	2.09
FBtr0086614	Phb2	2.09
FBtr0113248	Ire1	2.09
FBtr0306540	galectin	2.09
FBtr0110795	CG13624	2.09
FBtr0084672	CG13624	2.09
FBtr0339194	ETHR	2.09
FBtr0078611	Osi18	2.09
FBtr0076945	Prat2	2.09
FBtr0345204	CG13624	2.08
FBtr0084675	CG13624	2.08
FBtr0301733	galectin	2.08
FBtr0347271	CR43132	2.08
FBtr0086616	Phb2	2.07
FBtr0345716	CG2658	2.07
FBtr0070502	CG2658	2.07
FBtr0078484	CG7130	2.07
FBtr0087336	eIF2B-gamma	2.06
FBtr0077429	Traf4	2.06
FBtr0078517	CG14457	2.05
FBtr0080546	CenG1A	2.05
FBtr0301252	CG42553	2.03
FBtr0340059	Hmgs	2.03
FBtr0087149	Hmgs	2.03
FBtr0084182	CG5778	2.03
FBtr0344052	CR44987	2.02
FBtr0084304	Cyp6d4	2.02
FBtr0086677	GstE9	2.02
FBtr0337048	CG3999	2.02
FBtr0082225	CG3999	2.02
FBtr0344597	CR43130	2.02
FBtr0344598	CR43130	2.02
FBtr0112861	Phb2	2.01
FBtr0071827	Mes4	2.01
FBtr0301243	Mes4	2.01
FBtr0077586	CG3285	2.01
FBtr0339547	CG3285	2.01
FBtr0084403	unk	2.01
FBtr0079561	spz3	2.01
FBtr0081697	agt	2.01
FBtr0305571	unk	2.00
FBtr0075251	CG6512	1.99
FBtr0301455	Nipped-B	1.99
FBtr0301456	Nipped-B	1.99
FBtr0301454	Nipped-B	1.99
FBtr0083700	Xrp1	1.99
FBtr0345625	CR45311	1.99
FBtr0345624	CR45310	1.99
FBtr0290268	Sur	1.98
FBtr0335467	CG44140	1.98
FBtr0305998	bor	1.97
FBtr0083276	bor	1.97
FBtr0111118	Nipped-B	1.97
FBtr0111119	Nipped-B	1.97
FBtr0273232	CG10625	1.97
FBtr0332210	kek1	1.96
FBtr0307394	CG33969	1.96
FBtr0100010	CG33969	1.96
FBtr0084402	unk	1.96
FBtr0305572	unk	1.96
FBtr0273233	CG10625	1.96
FBtr0087518	pea	1.96
FBtr0075252	CG6512	1.95
FBtr0075656	CG16959	1.95
FBtr0087148	Hmgs	1.95
FBtr0335197	CG5778	1.95
FBtr0307520	CG5151	1.94
FBtr0300248	CG42458	1.94
FBtr0081690	Ccp84Ad	1.94
FBtr0083600	CG7142	1.94
FBtr0329896	mthl8	1.94
FBtr0301492	olf413	1.93
FBtr0085508	eIF2B-alpha	1.93
FBtr0074873	HLH106	1.93
FBtr0333877	HLH106	1.93
FBtr0074875	HLH106	1.93
FBtr0083542	sr	1.93
FBtr0330050	sr	1.93
FBtr0273231	CG10625	1.93
FBtr0345048	CR45171	1.93
FBtr0080656	CG15282	1.92
FBtr0112862	Phb2	1.92
FBtr0333219	olf413	1.92
FBtr0334994	Nipped-B	1.92
FBtr0074874	HLH106	1.92
FBtr0079477	Tep3	1.92
FBtr0081692	Ccp84Ab	1.92
FBtr0333935	CG16959	1.92
FBtr0305573	unk	1.92
FBtr0337052	unk	1.92
FBtr0071610	cv-2	1.92
FBtr0076193	Cpr67Fb	1.92
FBtr0075655	CG16959	1.91
FBtr0088463	GstT1	1.91
FBtr0301942	CG42402	1.91
FBtr0336454	CG42402	1.91
FBtr0072321	Cyp9c1	1.91
FBtr0073217	Ero1L	1.90
FBtr0346702	kek1	1.90
FBtr0303782	CG31955	1.90
FBtr0308925	CR31781	1.89
FBtr0308929	CR31781	1.89
FBtr0308926	CR31781	1.89
FBtr0346590	CR31781	1.89
FBtr0086906	Ns2	1.89
FBtr0331957	CR43787	1.89
FBtr0344633	sr	1.89
FBtr0083543	sr	1.89
FBtr0336664	Dpit47	1.89
FBtr0334401	Traf4	1.89
FBtr0342785	CR44691	1.89
FBtr0308927	CR31781	1.88
FBtr0346508	CG32152	1.88
FBtr0346525	CG5151	1.88
FBtr0307519	CG5151	1.88
FBtr0346507	CG32152	1.88
FBtr0307521	CG5151	1.88
FBtr0086146	Dpit47	1.88
FBtr0086820	CG30110	1.88
FBtr0300128	Cyp6a9	1.88
FBtr0303378	CG16959	1.87
FBtr0080891	CG17904	1.87
FBtr0078194	CG5872	1.87
FBtr0344821	CG5872	1.87
FBtr0075143	CG7402	1.87
FBtr0304797	CG13887	1.86
FBtr0331981	CG13565	1.86
FBtr0072605	CG13895	1.86
FBtr0331771	CG13895	1.86
FBtr0344053	CR44987	1.86
FBtr0081284	CG10189	1.86
FBtr0071038	CG3040	1.85
FBtr0072584	CG13887	1.85
FBtr0345588	CG13887	1.85
FBtr0087146	Hmgs	1.85
FBtr0087147	Hmgs	1.85
FBtr0087682	CG33156	1.85
FBtr0110781	CG11598	1.85
FBtr0071250	CG1785	1.85
FBtr0088957	Drat	1.85
FBtr0080290	CG12264	1.84
FBtr0087560	Arc1	1.84
FBtr0301109	Mp	1.84
FBtr0301106	Mp	1.84
FBtr0301107	Mp	1.84
FBtr0309957	Mp	1.84
FBtr0301114	Mp	1.84
FBtr0301105	Mp	1.84
FBtr0306638	Mp	1.84
FBtr0301113	Mp	1.84
FBtr0301111	Mp	1.84
FBtr0301108	Mp	1.84
FBtr0081541	Nlg1	1.84
FBtr0331327	CG10189	1.84
FBtr0301615	sr	1.84
FBtr0343270	Nxt1	1.84
FBtr0072241	Nxt1	1.84
FBtr0303445	CG31808	1.84
FBtr0084874	Cad96Ca	1.83
FBtr0072583	CG13887	1.83
FBtr0072129	ken	1.83
FBtr0301839	Ppn	1.83
FBtr0300337	Ppn	1.83
FBtr0301837	Ppn	1.83
FBtr0086892	P32	1.83
FBtr0072694	rho	1.83
FBtr0333207	rho	1.83
FBtr0073908	CG1461	1.83
FBtr0305969	Nlg1	1.83
FBtr0072563	Kah	1.83
FBtr0333578	mib1	1.83
FBtr0332144	ltl	1.82
FBtr0304066	f	1.82
FBtr0342730	CG11409	1.82
FBtr0340363	Bx	1.82
FBtr0301838	Ppn	1.82
FBtr0085410	ligatin	1.82
FBtr0339497	CG1461	1.82
FBtr0077366	CG12576	1.82
FBtr0339904	Mp	1.82
FBtr0113590	snoRNA:Psi28S-3405c	1.82
FBtr0075520	mib1	1.82
FBtr0299667	CG42287	1.81
FBtr0344235	CG16959	1.81
FBtr0339903	Mp	1.81
FBtr0301958	Mp	1.81
FBtr0343750	pre-mod(mdg4)-C	1.81
FBtr0339905	Mp	1.81
FBtr0340393	CG42306	1.80
FBtr0340392	Gint3	1.80
FBtr0332781	CR43868	1.80
FBtr0081200	CG31798	1.80
FBtr0334163	CG31798	1.80
FBtr0070763	XRCC1	1.80
FBtr0081374	La	1.80
FBtr0073202	Rcd5	1.80
FBtr0301110	Mp	1.80
FBtr0321322	snRNA:LU	1.80
FBtr0083779	CG17752	1.80
FBtr0088958	Drat	1.80
FBtr0299688	CG42306	1.79
FBtr0086654	Gint3	1.79
FBtr0299689	CG42306	1.79
FBtr0086655	Gint3	1.79
FBtr0076793	ltl	1.79
FBtr0113773	CG40002	1.79
FBtr0084116	CG6353	1.79
FBtr0086266	CG30148	1.79
FBtr0342706	CG30148	1.79
FBtr0073696	CG4407	1.79
FBtr0087456	Cyp6a21	1.79
FBtr0081218	CG17544	1.79
FBtr0088923	CG2064	1.79
FBtr0075394	mbf1	1.78
FBtr0344373	sima	1.78
FBtr0334300	CG33978	1.78
FBtr0310437	CG33978	1.78
FBtr0310435	CG33978	1.78
FBtr0084492	CG31142	1.78
FBtr0082074	P58IPK	1.78
FBtr0070366	Pgam5	1.78
FBtr0339601	Pgam5	1.78
FBtr0091708	scaRNA:MeU5-U42	1.78
FBtr0306159	CG43218	1.78
FBtr0080909	Ugt36Ba	1.78
FBtr0305570	mbf1	1.77
FBtr0075393	mbf1	1.77
FBtr0330137	mbf1	1.77
FBtr0080959	CG6115	1.77
FBtr0345447	CG6115	1.77
FBtr0075969	Gcn5	1.77
FBtr0070431	bcn92	1.77
FBtr0088146	sprt	1.77
FBtr0333151	CG4630	1.77
FBtr0305569	mbf1	1.76
FBtr0113494	snoRNA:Psi28S-2949	1.76
FBtr0075344	CG9674	1.76
FBtr0333608	CG9674	1.76
FBtr0305916	CG9674	1.76
FBtr0089699	Tim17b2	1.76
FBtr0343734	Tim17b2	1.76
FBtr0100653	Hsp67Bb	1.76
FBtr0087765	CG4630	1.76
FBtr0088863	Odc1	1.76
FBtr0072447	tRNA:CR30200	1.76
FBtr0081216	CG17544	1.76
FBtr0300822	CG17544	1.76
FBtr0081217	CG17544	1.76
FBtr0332780	CR43868	1.75
FBtr0345074	CG9674	1.75
FBtr0070961	CG14438	1.75
FBtr0072357	CG15873	1.75
FBtr0075519	mRpS31	1.75
FBtr0339539	babos	1.75
FBtr0071845	babos	1.75
FBtr0080104	CG31871	1.75
FBtr0088956	Drat	1.75
FBtr0336939	Drat	1.75
FBtr0080074	CG5604	1.74
FBtr0088882	CG8728	1.74
FBtr0078716	Atg17	1.74
FBtr0334946	Atg17	1.74
FBtr0345807	HBS1	1.74
FBtr0072866	HBS1	1.74
FBtr0070962	CG14438	1.74
FBtr0339464	CG14438	1.74
FBtr0078277	CG11399	1.74
FBtr0077580	CG15406	1.74
FBtr0303000	CG13062	1.74
FBtr0304481	mir-966	1.74
FBtr0309684	mir-4943	1.74
FBtr0077483	CG3714	1.73
FBtr0077482	CG3714	1.73
FBtr0310440	CG34422	1.73
FBtr0306541	CG11374	1.73
FBtr0300583	CG42494	1.73
FBtr0081205	CG9987	1.73
FBtr0340181	CR44396	1.73
FBtr0113020	CG3714	1.72
FBtr0336619	CG13077	1.72
FBtr0303473	Hsp67Bb	1.72
FBtr0072300	CG13581	1.72
FBtr0085370	Atg14	1.72
FBtr0085470	CG31041	1.72
FBtr0305483	CG43145	1.72
FBtr0307592	CG43386	1.72
FBtr0079868	CG17633	1.72
FBtr0345629	oys	1.71
FBtr0073763	Jafrac1	1.71
FBtr0339700	Jafrac1	1.71
FBtr0073764	Jafrac1	1.71
FBtr0339699	Jafrac1	1.71
FBtr0345161	Jafrac1	1.71
FBtr0302272	mtTFB1	1.71
FBtr0302271	Ccdc56	1.71
FBtr0303474	Hsp67Bb	1.71
FBtr0080837	CaBP1	1.71
FBtr0345544	CaBP1	1.71
FBtr0305619	CG10178	1.71
FBtr0072462	mthl8	1.71
FBtr0082765	CG9813	1.70
FBtr0335460	CG9813	1.70
FBtr0082768	CG9813	1.70
FBtr0082769	CG9813	1.70
FBtr0082766	CG9813	1.70
FBtr0082770	CG9813	1.70
FBtr0082767	CG9813	1.70
FBtr0302045	qm	1.70
FBtr0070141	Sec22	1.70
FBtr0310162	Sec22	1.70
FBtr0335046	CG12576	1.70
FBtr0077365	CG12576	1.70
FBtr0079464	santa-maria	1.70
FBtr0346571	santa-maria	1.70
FBtr0346429	CG12576	1.70
FBtr0075067	CG6843	1.70
FBtr0084053	ETHR	1.70
FBtr0081068	CG10178	1.70
FBtr0344041	CR44977	1.70
FBtr0331620	Ugt36Ba	1.70
FBtr0083724	CG14291	1.69
FBtr0332729	qm	1.69
FBtr0083703	Xrp1	1.69
FBtr0334523	Xrp1	1.69
FBtr0076846	qm	1.69
FBtr0302490	lft	1.69
FBtr0080002	lft	1.69
FBtr0333954	RhoGEF3	1.69
FBtr0333960	RhoGEF3	1.69
FBtr0333953	RhoGEF3	1.69
FBtr0081257	CG13077	1.69
FBtr0075240	Cad74A	1.69
FBtr0075239	Cad74A	1.69
FBtr0078631	CG10979	1.69
FBtr0335518	CG10979	1.69
FBtr0072966	CG16758	1.69
FBtr0081468	CG9253	1.69
FBtr0077481	CG3714	1.68
FBtr0345630	oys	1.68
FBtr0339416	oys	1.68
FBtr0088434	oys	1.68
FBtr0075341	CG9674	1.68
FBtr0333609	CG9674	1.68
FBtr0305915	CG9674	1.68
FBtr0333957	RhoGEF3	1.68
FBtr0333959	RhoGEF3	1.68
FBtr0333955	RhoGEF3	1.68
FBtr0302212	Kr-h2	1.68
FBtr0310365	CG34422	1.68
FBtr0345932	CG13565	1.68
FBtr0087681	CG33156	1.68
FBtr0347189	CG46025	1.68
FBtr0305649	CG33267	1.68
FBtr0307593	CG43386	1.68
FBtr0308759	CR43414	1.68
FBtr0086057	CG7791	1.67
FBtr0088901	Nop17l	1.67
FBtr0079602	CG14275	1.67
FBtr0334145	CG44009	1.67
FBtr0089767	gukh	1.66
FBtr0084368	CenB1A	1.66
FBtr0086893	CCHa1-R	1.66
FBtr0343126	Kr-h2	1.66
FBtr0079192	Kr-h2	1.66
FBtr0305961	dia	1.66
FBtr0086212	CG15237	1.66
FBtr0081157	l(2)37Ce	1.66
FBtr0087206	Rrp42	1.66
FBtr0075548	CG7272	1.66
FBtr0333614	CG5895	1.66
FBtr0100317	gukh	1.65
FBtr0083852	Xport	1.65
FBtr0310518	CG42508	1.65
FBtr0300643	CG42508	1.65
FBtr0113246	Xrp1	1.65
FBtr0343991	gukh	1.65
FBtr0070238	CG11409	1.65
FBtr0074095	Rhp	1.65
FBtr0088906	Cyt-b5	1.65
FBtr0309231	Cad74A	1.65
FBtr0303864	CR31144	1.65
FBtr0088349	Ndg	1.65
FBtr0339459	Ndg	1.65
FBtr0071108	Gclc	1.65
FBtr0340139	Gclc	1.65
FBtr0300775	CG1319	1.65
FBtr0339739	CR44340	1.65
FBtr0345052	CR45175	1.65
FBtr0076145	CG33268	1.65
FBtr0087205	CG8389	1.65
FBtr0336738	LysB	1.65
FBtr0072628	LysB	1.65
FBtr0346292	CR45611	1.65
FBtr0299668	CG42288	1.64
FBtr0307217	CG42288	1.64
FBtr0091659	CG33679	1.64
FBtr0084237	CG5382	1.64
FBtr0080358	CG6583	1.64
FBtr0084743	CG5805	1.64
FBtr0339255	CG5805	1.64
FBtr0074031	CG11655	1.64
FBtr0088212	Elp2	1.64
FBtr0087145	Hmgs	1.64
FBtr0308928	CR31781	1.64
FBtr0083277	mtSSB	1.64
FBtr0081438	RPA2	1.64
FBtr0333011	RPA2	1.64
FBtr0081449	CG14400	1.64
FBtr0083711	CG14285	1.64
FBtr0076347	Dronc	1.64
FBtr0273278	CG12379	1.64
FBtr0089768	gukh	1.63
FBtr0334283	Rgk1	1.63
FBtr0084017	meigo	1.63
FBtr0074096	Rhp	1.63
FBtr0088902	Nop17l	1.63
FBtr0077374	CG32500	1.63
FBtr0343751	pre-mod(mdg4)-AB	1.63
FBtr0343749	pre-mod(mdg4)-E	1.63
FBtr0343748	pre-mod(mdg4)-E	1.63
FBtr0076098	CG7394	1.63
FBtr0076604	CG7083	1.63
FBtr0310018	haf	1.63
FBtr0310020	haf	1.63
FBtr0310017	haf	1.63
FBtr0310019	haf	1.63
FBtr0082883	Nsf2	1.63
FBtr0344767	Nsf2	1.63
FBtr0344766	Nsf2	1.63
FBtr0073591	Sclp	1.63
FBtr0332672	CNMa	1.63
FBtr0300713	CNMa	1.63
FBtr0088592	Cyp4p1	1.63
FBtr0079429	CG31908	1.62
FBtr0345638	CG31908	1.62
FBtr0077480	CG3714	1.62
FBtr0077479	CG3714	1.62
FBtr0334792	CG3714	1.62
FBtr0083701	Xrp1	1.62
FBtr0334524	Xrp1	1.62
FBtr0331763	Alr	1.62
FBtr0113259	meigo	1.62
FBtr0304285	mir-281-1	1.62
FBtr0344846	brat	1.62
FBtr0081159	brat	1.62
FBtr0082347	RpL3	1.62
FBtr0081160	brat	1.62
FBtr0074989	Bet1	1.62
FBtr0332705	CG42575	1.62
FBtr0084279	CG33107	1.62
FBtr0081411	dia	1.62
FBtr0302658	CG42666	1.62
FBtr0340109	CG4313	1.62
FBtr0333409	CG31717	1.62
FBtr0334034	CG6769	1.62
FBtr0074493	CG6769	1.62
FBtr0344146	haf	1.62
FBtr0088789	Gasz	1.62
FBtr0340064	CG8303	1.62
FBtr0074799	Nup205	1.62
FBtr0301275	Larp7	1.62
FBtr0082679	Hsp70Ba	1.62
FBtr0079430	CG31908	1.61
FBtr0074300	eIF-2alpha	1.61
FBtr0343016	eIF-2alpha	1.61
FBtr0070425	Nmd3	1.61
FBtr0305648	CG7394	1.61
FBtr0333215	CG7394	1.61
FBtr0082410	CG10898	1.61
FBtr0302222	CG42615	1.61
FBtr0301134	CG5521	1.61
FBtr0085069	CG5521	1.61
FBtr0070460	gt	1.61
FBtr0081410	dia	1.61
FBtr0335145	dia	1.61
FBtr0344848	CG17104	1.61
FBtr0071107	Gclc	1.61
FBtr0340138	Gclc	1.61
FBtr0309969	CG42666	1.61
FBtr0331204	CG4213	1.61
FBtr0078093	CG4213	1.61
FBtr0072965	CG16758	1.61
FBtr0079977	CG31717	1.61
FBtr0340107	CG4313	1.61
FBtr0340162	p115	1.61
FBtr0071089	p115	1.61
FBtr0084201	CG7084	1.61
FBtr0085356	wdn	1.61
FBtr0072963	CG16758	1.61
FBtr0075437	CG5895	1.61
FBtr0087204	CG8389	1.61
FBtr0088760	Cyp4ad1	1.61
FBtr0334458	B-H2	1.61
FBtr0074429	B-H2	1.61
FBtr0074798	Nup205	1.61
FBtr0070140	CG16989	1.60
FBtr0343325	CG16989	1.60
FBtr0082325	Leash	1.60
FBtr0075338	Rh4	1.60
FBtr0085241	ALiX	1.60
FBtr0080105	CG17104	1.60
FBtr0336846	CG17104	1.60
FBtr0087418	CG8089	1.60
FBtr0079423	Pvf2	1.60
FBtr0075965	CG4069	1.60
FBtr0300863	List	1.60
FBtr0304745	CG7342	1.60
FBtr0083777	CG7342	1.60
FBtr0072964	CG16758	1.60
FBtr0301190	CG7084	1.60
FBtr0071928	Cyp6d2	1.60
FBtr0340065	CG8303	1.60
FBtr0071179	Corp	1.60
FBtr0307283	Corp	1.60
FBtr0085895	His-Psi:CR31614	1.60

2) Downregulated transcripts

Count: 1022 transcripts, matching to 642 genes

This table is related to Supplementary Table 3.

TDOWN_full_FC1.6 <- dPERK_full_join %>% filter (trans_reg == -1)
TDOWN_full_FC1.6_unq <- TDOWN_full_FC1.6  %>% dplyr::select(Gene.name) %>%  unique()
write.csv(TDOWN_full_FC1.6, "1.6_data_output/TDOWN_full_FC1.6.csv")
write.csv(TDOWN_full_FC1.6_unq, "1.6_data_output/TDOWN_full_FC1.6_unq.csv")

Table 2: Downregulated transcripts

Transcript ID	Gene ID	Transcript FC
FBtr0332792	syd	-1.60
FBtr0332789	syd	-1.60
FBtr0300412	syd	-1.60
FBtr0332787	syd	-1.60
FBtr0332790	syd	-1.60
FBtr0343591	CG2145	-1.60
FBtr0073387	CG2145	-1.60
FBtr0100323	fabp	-1.60
FBtr0100464	sea	-1.60
FBtr0345804	CG12974	-1.60
FBtr0332860	CG12974	-1.60
FBtr0078411	CG12974	-1.60
FBtr0086286	CG16739	-1.60
FBtr0071773	CG11291	-1.60
FBtr0339625	Chrac-16	-1.60
FBtr0073642	Chrac-16	-1.60
FBtr0302446	CG13492	-1.60
FBtr0075471	CG4962	-1.60
FBtr0299776	CG42323	-1.60
FBtr0086917	Lhr	-1.60
FBtr0086634	l(2)08717	-1.60
FBtr0290062	CG31812	-1.60
FBtr0073362	CG7509	-1.60
FBtr0114521	CG30051	-1.60
FBtr0344914	CR45133	-1.60
FBtr0100870	mt:ND3	-1.60
FBtr0113082	CG12963	-1.60
FBtr0302458	CG42658	-1.60
FBtr0085025	CG6503	-1.60
FBtr0302899	CG6503	-1.60
FBtr0309031	CG6503	-1.60
FBtr0081237	CG10026	-1.60
FBtr0081238	CG10026	-1.60
FBtr0332317	CG10026	-1.60
FBtr0080213	mre11	-1.60
FBtr0339415	CR44297	-1.60
FBtr0339251	CG13627	-1.60
FBtr0110944	CG34136	-1.60
FBtr0089324	Lsp2	-1.60
FBtr0345352	Lsp2	-1.60
FBtr0100860	mt:tRNA:Y	-1.60
FBtr0333382	CG6910	-1.61
FBtr0290130	CG6910	-1.61
FBtr0301707	Men-b	-1.61
FBtr0332788	syd	-1.61
FBtr0345912	syd	-1.61
FBtr0332791	syd	-1.61
FBtr0086258	qsm	-1.61
FBtr0074961	Oat	-1.61
FBtr0074509	Dhc16F	-1.61
FBtr0079526	CG14537	-1.61
FBtr0088579	GstE13	-1.61
FBtr0335462	CG9886	-1.61
FBtr0331355	CG15522	-1.61
FBtr0082290	Fdh	-1.61
FBtr0309986	CR43629	-1.61
FBtr0332394	CG8028	-1.61
FBtr0332393	CG8028	-1.61
FBtr0100321	fabp	-1.61
FBtr0086635	l(2)08717	-1.61
FBtr0345426	l(2)08717	-1.61
FBtr0300184	CG7231	-1.61
FBtr0304902	CG13203	-1.61
FBtr0334105	CG7255	-1.61
FBtr0304119	Lip4	-1.61
FBtr0344047	CR44982	-1.61
FBtr0332817	CG43896	-1.61
FBtr0345688	CG43896	-1.61
FBtr0110814	CG15661	-1.61
FBtr0076589	CG13311	-1.61
FBtr0305612	CR43158	-1.61
FBtr0070866	CG5966	-1.61
FBtr0343294	CG5966	-1.61
FBtr0079058	mRpL24	-1.62
FBtr0080212	Ppt2	-1.62
FBtr0343011	CG13516	-1.62
FBtr0100554	CG13516	-1.62
FBtr0077751	CG4267	-1.62
FBtr0081550	alpha-Est7	-1.62
FBtr0085503	CG15522	-1.62
FBtr0100320	fabp	-1.62
FBtr0306336	CG7231	-1.62
FBtr0079531	CG7231	-1.62
FBtr0073473	CG15199	-1.62
FBtr0344246	CR45024	-1.62
FBtr0084918	CG31380	-1.62
FBtr0071624	CG15661	-1.62
FBtr0083140	Spn88Eb	-1.62
FBtr0078025	Lsp1beta	-1.62
FBtr0345738	Lsp1beta	-1.62
FBtr0084317	CG4721	-1.63
FBtr0073555	m	-1.63
FBtr0344884	CR9284	-1.63
FBtr0070558	CG3603	-1.63
FBtr0299774	CG42323	-1.63
FBtr0345485	Cyp6w1	-1.63
FBtr0085987	Cyp6w1	-1.63
FBtr0113197	CG1208	-1.63
FBtr0084038	r-l	-1.63
FBtr0088176	dare	-1.63
FBtr0083615	CG14313	-1.63
FBtr0089608	Dup99B	-1.63
FBtr0347179	CR11538	-1.63
FBtr0076769	syd	-1.64
FBtr0300413	syd	-1.64
FBtr0087906	CG30049	-1.64
FBtr0344893	LRP1	-1.64
FBtr0304022	CG42806	-1.64
FBtr0082715	CG7966	-1.64
FBtr0082776	CG15887	-1.64
FBtr0343596	CG5321	-1.64
FBtr0084548	Npc2f	-1.64
FBtr0305053	Dup99B	-1.64
FBtr0344894	LRP1	-1.65
FBtr0306574	CG6805	-1.65
FBtr0084101	CG3301	-1.65
FBtr0100481	CG9510	-1.65
FBtr0340263	CG9510	-1.65
FBtr0299780	CG9510	-1.65
FBtr0085213	CG5402	-1.65
FBtr0100088	CG34033	-1.65
FBtr0079857	Mtpalpha	-1.65
FBtr0308944	CR9284	-1.65
FBtr0309648	mir-4954	-1.65
FBtr0331635	CG5853	-1.65
FBtr0345347	CG13026	-1.65
FBtr0113405	CG31414	-1.65
FBtr0334767	CG31414	-1.65
FBtr0081321	fbp	-1.65
FBtr0084292	CG5376	-1.65
FBtr0340008	CR44370	-1.65
FBtr0340009	CR44370	-1.65
FBtr0075187	CG7460	-1.66
FBtr0074445	CG8664	-1.66
FBtr0339779	CG8664	-1.66
FBtr0075895	AdenoK	-1.66
FBtr0346531	AdenoK	-1.66
FBtr0086299	CG11200	-1.66
FBtr0339195	CG3301	-1.66
FBtr0344185	CG11200	-1.66
FBtr0079858	Mtpalpha	-1.66
FBtr0332040	CG12182	-1.66
FBtr0072255	Dat	-1.66
FBtr0072393	CG3770	-1.66
FBtr0299542	CG13026	-1.66
FBtr0342721	CG16799	-1.66
FBtr0086249	CG16799	-1.66
FBtr0343856	fbp	-1.66
FBtr0309068	CR43434	-1.66
FBtr0307213	ventrally-expressed-protein-D	-1.66
FBtr0082625	CG4830	-1.66
FBtr0331991	CG13397	-1.66
FBtr0303856	CR42836	-1.66
FBtr0340638	CR44511	-1.66
FBtr0332816	CG43896	-1.66
FBtr0075744	CG13482	-1.66
FBtr0339240	CG14245	-1.66
FBtr0089685	CRMP	-1.67
FBtr0070115	CG13369	-1.67
FBtr0078504	CG11438	-1.67
FBtr0345586	CG11438	-1.67
FBtr0075637	CG13458	-1.67
FBtr0087702	arr	-1.67
FBtr0086300	CG11200	-1.67
FBtr0079894	CG5853	-1.67
FBtr0345615	CG5853	-1.67
FBtr0343502	CG3770	-1.67
FBtr0080937	CG17996	-1.67
FBtr0088467	CG1773	-1.67
FBtr0113583	snoRNA:Psi18S-301	-1.67
FBtr0086853	snoRNA:U31:54Eb	-1.67
FBtr0079711	CG13397	-1.67
FBtr0343003	CR42868	-1.67
FBtr0073405	Ork1	-1.67
FBtr0079469	CG5149	-1.67
FBtr0345642	CR43239	-1.67
FBtr0339798	CR43239	-1.67
FBtr0306294	CR43239	-1.67
FBtr0100553	CG14245	-1.67
FBtr0310393	CR43669	-1.67
FBtr0089686	CRMP	-1.68
FBtr0114453	CRMP	-1.68
FBtr0075017	CG9629	-1.68
FBtr0333692	CG7460	-1.68
FBtr0086966	CG6805	-1.68
FBtr0091697	snoRNA:Psi28S-3186	-1.68
FBtr0073015	CG12093	-1.68
FBtr0075223	qjt	-1.68
FBtr0079242	Ugt37b1	-1.68
FBtr0307037	fusl	-1.68
FBtr0079078	fusl	-1.68
FBtr0084259	CG7046	-1.68
FBtr0100862	mt:tRNA:L:UUR	-1.68
FBtr0113334	CG14132	-1.69
FBtr0330647	Amnionless	-1.69
FBtr0079485	CG7191	-1.69
FBtr0343400	CG7191	-1.69
FBtr0332493	CG3603	-1.69
FBtr0078195	CG5910	-1.69
FBtr0302854	Phae2	-1.69
FBtr0345718	Phae2	-1.69
FBtr0301483	CG7046	-1.69
FBtr0077557	odd	-1.69
FBtr0088133	CG7759	-1.69
FBtr0113596	snoRNA:Psi18S-1377c	-1.69
FBtr0072062	Dcp-1	-1.70
FBtr0346480	CG16772	-1.70
FBtr0081302	CG16772	-1.70
FBtr0289953	alpha-Est10	-1.70
FBtr0072955	CG12182	-1.70
FBtr0077973	CG5011	-1.70
FBtr0335382	CG5011	-1.70
FBtr0075459	l(3)72Dp	-1.70
FBtr0339901	CG32320	-1.70
FBtr0310142	CG12910	-1.70
FBtr0310469	CG42790	-1.70
FBtr0082026	CG8129	-1.70
FBtr0076832	Cyp4d8	-1.70
FBtr0303855	CR42836	-1.70
FBtr0346624	bgm	-1.70
FBtr0080590	bgm	-1.70
FBtr0114456	Hr51	-1.70
FBtr0306697	CG12224	-1.70
FBtr0335436	CG12224	-1.70
FBtr0075127	CG7330	-1.70
FBtr0332861	CG7330	-1.70
FBtr0077863	CG15353	-1.71
FBtr0075040	CG18136	-1.71
FBtr0307504	CG18814	-1.71
FBtr0075896	AdenoK	-1.71
FBtr0075465	CG13067	-1.71
FBtr0087622	CG16935	-1.71
FBtr0073208	CG14990	-1.71
FBtr0077770	CG9886	-1.71
FBtr0073284	CG11594	-1.71
FBtr0083370	CG3534	-1.71
FBtr0071779	Oatp58Da	-1.71
FBtr0113196	CG1208	-1.71
FBtr0078454	CG14567	-1.71
FBtr0346304	Ork1	-1.71
FBtr0073404	Ork1	-1.71
FBtr0343584	Ork1	-1.71
FBtr0087291	CG8299	-1.71
FBtr0346492	CR45712	-1.72
FBtr0077884	CG31937	-1.72
FBtr0085215	CG5590	-1.72
FBtr0100833	CG34056	-1.72
FBtr0339954	CG16935	-1.72
FBtr0346795	CG33082	-1.72
FBtr0300818	CG17324	-1.72
FBtr0075190	Adgf-A	-1.72
FBtr0075191	Adgf-A	-1.72
FBtr0081734	CG1041	-1.72
FBtr0086821	CG30325	-1.72
FBtr0114353	snoRNA:Me18S-G962	-1.72
FBtr0321259	CG5322	-1.72
FBtr0342643	CG42876	-1.72
FBtr0304142	CG42876	-1.72
FBtr0080224	CG31867	-1.72
FBtr0080539	CAH1	-1.73
FBtr0300691	Kdm2	-1.73
FBtr0077542	CG31777	-1.73
FBtr0081881	CG8036	-1.73
FBtr0334521	CG14298	-1.73
FBtr0083695	CG14298	-1.73
FBtr0347031	Ccy	-1.73
FBtr0078134	Amnionless	-1.73
FBtr0347061	CG11241	-1.73
FBtr0079491	LanB1	-1.73
FBtr0110774	CG1041	-1.73
FBtr0344293	CG1041	-1.73
FBtr0347005	CG1041	-1.73
FBtr0087463	NaPi-T	-1.73
FBtr0343768	yellow-b	-1.73
FBtr0080894	yellow-b	-1.73
FBtr0082101	Fst	-1.73
FBtr0084100	CG3301	-1.74
FBtr0113389	CG31103	-1.74
FBtr0336758	Kdm2	-1.74
FBtr0072561	Reg-2	-1.74
FBtr0332429	CG15515	-1.74
FBtr0300411	CG5910	-1.74
FBtr0345717	Phae1	-1.74
FBtr0300301	CG42465	-1.74
FBtr0088337	CG12910	-1.74
FBtr0076510	GNBP3	-1.74
FBtr0308768	CR43419	-1.74
FBtr0329884	NaPi-T	-1.74
FBtr0310051	qjt	-1.74
FBtr0339534	ventrally-expressed-protein-D	-1.74
FBtr0071826	ventrally-expressed-protein-D	-1.74
FBtr0110771	Spn75F	-1.74
FBtr0080042	CG5322	-1.74
FBtr0336759	Kdm2	-1.75
FBtr0336760	Kdm2	-1.75
FBtr0081882	CG8036	-1.75
FBtr0304891	CG43103	-1.75
FBtr0087420	Obp51a	-1.75
FBtr0112749	CG34445	-1.75
FBtr0076316	CG14160	-1.75
FBtr0336865	CR44182	-1.75
FBtr0299856	CG42336	-1.75
FBtr0079751	CG9289	-1.75
FBtr0346275	CG2444	-1.75
FBtr0073531	CG2444	-1.75
FBtr0305896	CG43167	-1.75
FBtr0070913	Spat	-1.75
FBtr0343627	CG31867	-1.75
FBtr0087014	tef	-1.75
FBtr0307596	CG13827	-1.76
FBtr0076905	CG14823	-1.76
FBtr0086640	CG15093	-1.76
FBtr0082902	CG9649	-1.76
FBtr0342844	CR44705	-1.76
FBtr0081077	Cyp310a1	-1.76
FBtr0078556	slif	-1.76
FBtr0310046	CG11594	-1.76
FBtr0082027	CG8129	-1.76
FBtr0346572	CG31821	-1.76
FBtr0080809	CG31821	-1.76
FBtr0340252	CR44413	-1.76
FBtr0085307	CG9989	-1.76
FBtr0087954	CG8834	-1.76
FBtr0082969	BigH1	-1.76
FBtr0344540	SclB	-1.77
FBtr0344543	SclA	-1.77
FBtr0344541	SclB	-1.77
FBtr0344544	SclA	-1.77
FBtr0334005	CG10062	-1.77
FBtr0086522	CG10062	-1.77
FBtr0088502	CG12926	-1.77
FBtr0086639	CG15093	-1.77
FBtr0303846	CG15093	-1.77
FBtr0078555	slif	-1.77
FBtr0078206	CG18281	-1.77
FBtr0080255	Vha100-5	-1.77
FBtr0335471	Vha100-5	-1.77
FBtr0307189	CG15199	-1.77
FBtr0075975	CG10657	-1.77
FBtr0336709	TwdlG	-1.77
FBtr0084486	CG10182	-1.77
FBtr0334006	CG10062	-1.78
FBtr0309192	CR43458	-1.78
FBtr0081883	CG8036	-1.78
FBtr0080334	Phae1	-1.78
FBtr0078557	slif	-1.78
FBtr0073283	CG11594	-1.78
FBtr0086292	Obp57c	-1.78
FBtr0113516	snoRNA:Psi28S-3316a	-1.78
FBtr0305591	CG3775	-1.78
FBtr0073690	CG3775	-1.78
FBtr0303218	CG14607	-1.78
FBtr0078005	CG13947	-1.78
FBtr0346432	CR45682	-1.78
FBtr0079055	Jon25Bii	-1.78
FBtr0345335	Jon25Bii	-1.78
FBtr0113436	CG32425	-1.79
FBtr0303818	CG42808	-1.79
FBtr0084376	CG13827	-1.79
FBtr0073237	Hexo1	-1.79
FBtr0071338	su(r)	-1.79
FBtr0081251	CG13082	-1.79
FBtr0300655	CG42514	-1.79
FBtr0299610	CG42269	-1.79
FBtr0086986	Gbp	-1.79
FBtr0335458	CG14377	-1.79
FBtr0344542	SclB	-1.80
FBtr0344539	SclB	-1.80
FBtr0078204	CG32425	-1.80
FBtr0300774	Hexo1	-1.80
FBtr0333776	CR43964	-1.80
FBtr0070175	CG14630	-1.80
FBtr0309791	CG11594	-1.80
FBtr0303377	CG31664	-1.80
FBtr0334829	CG31664	-1.80
FBtr0081439	Mtp	-1.80
FBtr0080273	CG31704	-1.80
FBtr0333421	CG31704	-1.80
FBtr0345152	CR45192	-1.80
FBtr0345151	CR45192	-1.80
FBtr0086935	CG4847	-1.80
FBtr0086934	CG4847	-1.80
FBtr0086933	CG4847	-1.80
FBtr0086937	CG4847	-1.80
FBtr0334151	CG44013	-1.80
FBtr0334150	CG44013	-1.80
FBtr0346519	CG42512	-1.81
FBtr0342579	CG16964	-1.81
FBtr0080282	CG16964	-1.81
FBtr0084863	CG31098	-1.81
FBtr0077700	CG9879	-1.81
FBtr0077671	CG17224	-1.81
FBtr0308618	eas	-1.81
FBtr0333189	CG40198	-1.81
FBtr0301809	CG40198	-1.81
FBtr0086854	snoRNA:U31:54Ec	-1.81
FBtr0344126	CR45013	-1.81
FBtr0077997	CG4375	-1.82
FBtr0079984	CG4953	-1.82
FBtr0333820	CG1969	-1.82
FBtr0330296	CG1969	-1.82
FBtr0085474	CG1969	-1.82
FBtr0345371	CG13321	-1.82
FBtr0087792	CG13321	-1.82
FBtr0082259	Irp-1B	-1.82
FBtr0300761	CG12560	-1.82
FBtr0310267	CG1969	-1.82
FBtr0083790	CG11407	-1.82
FBtr0083278	CG6126	-1.82
FBtr0300815	CG17224	-1.82
FBtr0300656	CG42514	-1.82
FBtr0100007	CG33966	-1.82
FBtr0080006	CG5096	-1.83
FBtr0071611	CG17974	-1.83
FBtr0333567	Hexo1	-1.83
FBtr0073235	Hexo1	-1.83
FBtr0077672	CG17224	-1.83
FBtr0310457	CG43679	-1.83
FBtr0310456	CG43679	-1.83
FBtr0309300	CR43471	-1.83
FBtr0300657	CG42514	-1.83
FBtr0085755	CG1544	-1.83
FBtr0078221	ZnT77C	-1.83
FBtr0077544	CG10031	-1.83
FBtr0079768	Toll-4	-1.83
FBtr0083780	CG16727	-1.83
FBtr0091959	pncr015:3L	-1.83
FBtr0343908	CR44938	-1.83
FBtr0072254	Dat	-1.84
FBtr0078298	CG10512	-1.84
FBtr0112403	CG34210	-1.84
FBtr0085475	CG1969	-1.84
FBtr0333821	CG1969	-1.84
FBtr0085766	CG11340	-1.84
FBtr0077942	NLaz	-1.84
FBtr0343844	NLaz	-1.84
FBtr0329947	NLaz	-1.84
FBtr0331629	CG17224	-1.84
FBtr0332297	CG11816	-1.84
FBtr0332774	CR43872	-1.84
FBtr0310470	CG42790	-1.84
FBtr0085649	CDase	-1.84
FBtr0290201	CG15553	-1.84
FBtr0344545	SclA	-1.85
FBtr0071625	CG4302	-1.85
FBtr0306104	CG1969	-1.85
FBtr0343383	CG12560	-1.85
FBtr0347182	mdy	-1.85
FBtr0332298	CG11816	-1.85
FBtr0082025	CG18473	-1.85
FBtr0085647	CDase	-1.85
FBtr0085648	CDase	-1.85
FBtr0085101	TwdlT	-1.85
FBtr0331816	Spn77Bc	-1.85
FBtr0078172	Spn77Bc	-1.85
FBtr0072091	CG5532	-1.86
FBtr0345535	CG5532	-1.86
FBtr0333446	CG1246	-1.86
FBtr0072938	CG1246	-1.86
FBtr0303022	CG1246	-1.86
FBtr0310141	CG12910	-1.86
FBtr0072556	Gale	-1.87
FBtr0078297	CG10512	-1.87
FBtr0302718	Cpr47Ef	-1.87
FBtr0302719	Cpr47Ef	-1.87
FBtr0345027	CG1246	-1.87
FBtr0085646	CDase	-1.87
FBtr0078220	ZnT77C	-1.87
FBtr0085861	CG2187	-1.87
FBtr0300408	CG34043	-1.87
FBtr0306917	Gale	-1.88
FBtr0100356	Spn43Ab	-1.88
FBtr0077588	CG8838	-1.88
FBtr0070186	CG3699	-1.88
FBtr0345610	CG16712	-1.88
FBtr0077546	CG16712	-1.88
FBtr0074212	eas	-1.88
FBtr0339106	CG44251	-1.88
FBtr0085645	CDase	-1.88
FBtr0075942	CG10960	-1.88
FBtr0075942	CG10960	-1.88
FBtr0334776	CR44054	-1.88
FBtr0073474	ssp7	-1.88
FBtr0344128	CR43936	-1.88
FBtr0083026	CG3987	-1.88
FBtr0302527	CG33346	-1.88
FBtr0083510	Lgr1	-1.89
FBtr0073322	CG32243	-1.89
FBtr0347018	CR45925	-1.89
FBtr0340495	Vsx1	-1.89
FBtr0070781	Vsx1	-1.89
FBtr0078300	CG10512	-1.89
FBtr0075076	CG3902	-1.89
FBtr0080566	mRpS23	-1.89
FBtr0077310	GstT3	-1.89
FBtr0075699	bmm	-1.89
FBtr0300190	bmm	-1.89
FBtr0334830	CR44076	-1.89
FBtr0100857	mt:ND2	-1.89
FBtr0289973	CG13905	-1.89
FBtr0078299	CG10512	-1.90
FBtr0070844	CG33080	-1.90
FBtr0342971	CG33080	-1.90
FBtr0308619	eas	-1.90
FBtr0080917	mdy	-1.90
FBtr0073785	CG11816	-1.90
FBtr0331357	CDase	-1.90
FBtr0345735	CR45341	-1.90
FBtr0303376	CG2187	-1.90
FBtr0075750	Fbp1	-1.90
FBtr0339515	Fbp1	-1.90
FBtr0075749	Fbp1	-1.90
FBtr0332135	CG7201	-1.90
FBtr0076527	Tequila	-1.91
FBtr0303835	CG42828	-1.91
FBtr0080915	mdy	-1.91
FBtr0302029	CG14946	-1.91
FBtr0070088	arg	-1.91
FBtr0339107	CG44251	-1.91
FBtr0345617	CG7300	-1.91
FBtr0336849	CR44181	-1.91
FBtr0080125	CG7300	-1.91
FBtr0088184	TpnC47D	-1.91
FBtr0345540	TpnC47D	-1.91
FBtr0339346	CG42326	-1.91
FBtr0079438	gudu	-1.91
FBtr0071600	CG9485	-1.92
FBtr0300394	CG9485	-1.92
FBtr0071599	CG9485	-1.92
FBtr0343519	eas	-1.92
FBtr0074211	eas	-1.92
FBtr0074214	eas	-1.92
FBtr0080916	mdy	-1.92
FBtr0080095	CG18302	-1.92
FBtr0087935	CG8550	-1.92
FBtr0339398	AdamTS-A	-1.92
FBtr0334629	AdamTS-A	-1.92
FBtr0331736	CG11816	-1.92
FBtr0335261	CR42646	-1.92
FBtr0302350	CR42646	-1.92
FBtr0084853	CG10553	-1.92
FBtr0080549	CG7916	-1.92
FBtr0086667	CG15065	-1.92
FBtr0083509	Lgr1	-1.93
FBtr0071601	CG9485	-1.93
FBtr0300395	CG9485	-1.93
FBtr0310327	CG9485	-1.93
FBtr0343520	eas	-1.93
FBtr0308617	eas	-1.93
FBtr0305265	CG14946	-1.93
FBtr0342607	CG14946	-1.93
FBtr0308830	CG6294	-1.93
FBtr0083160	AdamTS-A	-1.93
FBtr0332794	CR43893	-1.93
FBtr0273320	CG13024	-1.93
FBtr0340430	CG44426	-1.93
FBtr0074444	CG8661	-1.93
FBtr0082981	CG8066	-1.94
FBtr0309193	CR43458	-1.94
FBtr0334312	tsl	-1.94
FBtr0084164	tsl	-1.94
FBtr0309099	CG9837	-1.94
FBtr0336680	St3	-1.95
FBtr0113345	CG18748	-1.95
FBtr0346481	CR45701	-1.95
FBtr0084352	CG6733	-1.95
FBtr0083755	CG3734	-1.95
FBtr0083329	CG17562	-1.96
FBtr0070201	CG11380	-1.96
FBtr0345506	CG11380	-1.96
FBtr0343860	scw	-1.96
FBtr0081261	scw	-1.96
FBtr0079466	CG5958	-1.96
FBtr0339152	CG3734	-1.96
FBtr0334331	CG9837	-1.96
FBtr0076716	CG7201	-1.96
FBtr0080573	adat	-1.97
FBtr0300132	CG11891	-1.97
FBtr0300959	fa2h	-1.97
FBtr0113188	CG11241	-1.97
FBtr0072599	CG13898	-1.97
FBtr0345489	Mal-A7	-1.98
FBtr0088757	Mal-A7	-1.98
FBtr0086972	CG9640	-1.98
FBtr0078536	CG11241	-1.98
FBtr0070806	CG15773	-1.98
FBtr0081303	CG10680	-1.99
FBtr0332182	CG10680	-1.99
FBtr0072635	CG9119	-1.99
FBtr0084165	tsl	-1.99
FBtr0113344	CG18748	-1.99
FBtr0339631	Cpr49Ac	-1.99
FBtr0086807	CG10912	-1.99
FBtr0084056	CG17298	-1.99
FBtr0075091	Cyp12c1	-2.00
FBtr0345812	Cyp12c1	-2.00
FBtr0085737	CG15556	-2.00
FBtr0071733	CG13494	-2.00
FBtr0334571	Ela	-2.00
FBtr0084708	Ela	-2.00
FBtr0309098	CG9837	-2.00
FBtr0087514	Cpr51A	-2.01
FBtr0345306	sxe2	-2.01
FBtr0087916	Cpr49Ac	-2.01
FBtr0299788	CG42326	-2.01
FBtr0344981	Tequila	-2.02
FBtr0076525	Tequila	-2.02
FBtr0309195	CG15556	-2.02
FBtr0332253	CR43810	-2.02
FBtr0071240	CG12116	-2.02
FBtr0083225	sxe2	-2.02
FBtr0343666	CG7953	-2.02
FBtr0080550	CG7953	-2.02
FBtr0334959	CG8066	-2.03
FBtr0309194	CG15556	-2.03
FBtr0079607	Mur29B	-2.03
FBtr0086123	CG3270	-2.03
FBtr0080093	Lip4	-2.03
FBtr0088204	CG13230	-2.03
FBtr0339104	CG44250	-2.03
FBtr0339105	CG44250	-2.03
FBtr0301372	Cpr49Ac	-2.03
FBtr0344129	CR43936	-2.03
FBtr0339490	CG44303	-2.03
FBtr0347095	CR45978	-2.03
FBtr0075943	CG10960	-2.04
FBtr0075941	CG10960	-2.04
FBtr0087917	Cpr49Ac	-2.04
FBtr0339630	Cpr49Ac	-2.04
FBtr0074843	Spn77Bb	-2.04
FBtr0078315	CG33056	-2.05
FBtr0078311	CG33056	-2.05
FBtr0084824	CG31300	-2.05
FBtr0079339	CG11236	-2.05
FBtr0309812	CG11236	-2.05
FBtr0078312	CG33056	-2.06
FBtr0336460	CG14526	-2.06
FBtr0071607	Acox57D-d	-2.06
FBtr0084709	Ela	-2.06
FBtr0078314	CG33056	-2.07
FBtr0075511	CG17032	-2.07
FBtr0308817	CG8249	-2.07
FBtr0080127	CG17108	-2.07
FBtr0347273	CR46058	-2.07
FBtr0071472	Gip	-2.08
FBtr0340044	GstT3	-2.08
FBtr0300210	GstT3	-2.08
FBtr0100230	CG18003	-2.08
FBtr0302916	Ir60c	-2.08
FBtr0071832	CG4752	-2.09
FBtr0089053	Spn43Ad	-2.09
FBtr0070423	CG18031	-2.09
FBtr0330695	CG43755	-2.10
FBtr0333574	CG17032	-2.10
FBtr0309709	mir-4914	-2.10
FBtr0112396	CG34203	-2.10
FBtr0077163	CG15212	-2.10
FBtr0331672	Lip4	-2.10
FBtr0305913	CG13024	-2.10
FBtr0078313	CG33056	-2.11
FBtr0075321	CG9701	-2.11
FBtr0300308	CG42470	-2.11
FBtr0309185	CR43452	-2.11
FBtr0080564	CG33306	-2.11
FBtr0084255	Pebp1	-2.11
FBtr0304880	CG43092	-2.12
FBtr0300709	CG13795	-2.13
FBtr0343407	CG13795	-2.13
FBtr0082323	CG6465	-2.13
FBtr0084634	CG5715	-2.13
FBtr0344980	Tequila	-2.14
FBtr0082179	CG3940	-2.14
FBtr0344391	CG3940	-2.14
FBtr0344392	CG3940	-2.14
FBtr0343602	CG12715	-2.14
FBtr0073750	CG12715	-2.14
FBtr0072768	Gk	-2.14
FBtr0072767	Gk	-2.14
FBtr0345817	Gk	-2.14
FBtr0085966	CG7882	-2.14
FBtr0335266	CG7882	-2.14
FBtr0087117	Amyrel	-2.14
FBtr0079495	LKR	-2.14
FBtr0343404	LKR	-2.14
FBtr0300805	CG18284	-2.15
FBtr0339130	CG18284	-2.15
FBtr0343380	CG9509	-2.15
FBtr0073978	CG9509	-2.15
FBtr0084151	dnd	-2.16
FBtr0070845	CG33080	-2.16
FBtr0072769	Gk	-2.16
FBtr0088759	Mal-A1	-2.17
FBtr0079322	Galt	-2.17
FBtr0333352	Galt	-2.17
FBtr0305959	CG17374	-2.17
FBtr0342972	CG33080	-2.17
FBtr0083106	CG6125	-2.17
FBtr0082506	CG18547	-2.18
FBtr0345120	TpnC73F	-2.18
FBtr0089585	TpnC73F	-2.18
FBtr0332548	CR43846	-2.18
FBtr0307187	CG15202	-2.18
FBtr0083105	CG6125	-2.18
FBtr0346109	CG6125	-2.18
FBtr0070490	w	-2.19
FBtr0091499	lectin-37Db	-2.19
FBtr0302362	lectin-37Db	-2.19
FBtr0100869	mt:tRNA:G	-2.19
FBtr0307505	CG31076	-2.20
FBtr0082111	CG9396	-2.21
FBtr0073438	CG15202	-2.21
FBtr0110768	Acp54A1	-2.21
FBtr0072770	Gk	-2.22
FBtr0333800	CG4020	-2.22
FBtr0070824	CG4020	-2.22
FBtr0073651	Lsp1alpha	-2.22
FBtr0082143	CG8534	-2.22
FBtr0310421	alpha-Est2	-2.23
FBtr0071560	CG9993	-2.23
FBtr0334683	CR44035	-2.23
FBtr0081540	alpha-Est2	-2.24
FBtr0077791	CG3609	-2.24
FBtr0331441	CG3609	-2.24
FBtr0303027	CG3609	-2.25
FBtr0100144	pug	-2.25
FBtr0082264	pug	-2.25
FBtr0308753	CR43411	-2.25
FBtr0300296	Sfp24Ba	-2.25
FBtr0082565	CG17738	-2.25
FBtr0308818	CG8249	-2.26
FBtr0079073	TotM	-2.26
FBtr0085329	CG14528	-2.27
FBtr0336635	CG9864	-2.27
FBtr0086320	CG9864	-2.27
FBtr0084431	CG4408	-2.27
FBtr0339619	CG4408	-2.27
FBtr0113600	snoRNA:Psi18S-110	-2.27
FBtr0307036	TotM	-2.27
FBtr0336678	St3	-2.28
FBtr0078848	CG14661	-2.29
FBtr0305965	CG14661	-2.29
FBtr0079066	Cyp4ac1	-2.29
FBtr0082265	pug	-2.29
FBtr0082266	pug	-2.29
FBtr0305662	pug	-2.29
FBtr0074559	Tsf1	-2.29
FBtr0346625	Tsf1	-2.29
FBtr0299796	CG42329	-2.29
FBtr0343671	CG8997	-2.29
FBtr0080563	CG8997	-2.29
FBtr0071123	CG2233	-2.30
FBtr0072929	CG16985	-2.30
FBtr0302992	CG9465	-2.31
FBtr0336679	St3	-2.31
FBtr0087310	CG8249	-2.31
FBtr0080693	dyn-p25	-2.32
FBtr0332601	CR43866	-2.32
FBtr0075157	CG5506	-2.32
FBtr0304645	CG43061	-2.32
FBtr0076914	CG8628	-2.32
FBtr0301218	CG8628	-2.32
FBtr0330696	CG43755	-2.33
FBtr0076003	Est-6	-2.33
FBtr0333383	Est-6	-2.33
FBtr0085472	CG7567	-2.33
FBtr0078644	CG1213	-2.34
FBtr0307274	alpha-Est5	-2.34
FBtr0074494	CG12985	-2.34
FBtr0344411	CG31517	-2.34
FBtr0078642	CG1213	-2.35
FBtr0072771	Gk	-2.35
FBtr0079741	CG9468	-2.35
FBtr0082864	CG31517	-2.35
FBtr0088752	Mal-A8	-2.36
FBtr0340616	CG5162	-2.36
FBtr0074393	CG5162	-2.36
FBtr0347303	CR46074	-2.36
FBtr0077212	Cyp6t1	-2.36
FBtr0081547	alpha-Est5	-2.37
FBtr0082651	Gnmt	-2.37
FBtr0087399	Hex-C	-2.38
FBtr0332376	UK114	-2.38
FBtr0083330	CG17560	-2.39
FBtr0086134	CG9436	-2.39
FBtr0305954	CG1213	-2.40
FBtr0078643	CG1213	-2.40
FBtr0087171	CG7997	-2.40
FBtr0080746	UK114	-2.40
FBtr0336977	CG3679	-2.40
FBtr0078656	Obp83a	-2.40
FBtr0309293	CR43468	-2.41
FBtr0087172	CG7997	-2.42
FBtr0300902	CG18563	-2.42
FBtr0087042	CG6426	-2.43
FBtr0346581	CG3604	-2.43
FBtr0079230	Gal	-2.43
FBtr0332603	Gal	-2.43
FBtr0345251	Obp83a	-2.43
FBtr0079282	CG9498	-2.43
FBtr0114541	St1	-2.44
FBtr0077689	CG18557	-2.45
FBtr0339575	CG16704	-2.46
FBtr0077550	CG16704	-2.46
FBtr0081102	CG17325	-2.47
FBtr0299687	CG42305	-2.47
FBtr0087813	CG3814	-2.47
FBtr0077141	CG13285	-2.48
FBtr0073961	dob	-2.48
FBtr0075434	CG13043	-2.49
FBtr0345443	CG17325	-2.49
FBtr0299685	CG17325	-2.49
FBtr0345444	CG42305	-2.49
FBtr0299686	CG42305	-2.49
FBtr0077545	CG3604	-2.49
FBtr0075221	CG7589	-2.49
FBtr0333690	CG7589	-2.49
FBtr0087814	CG3814	-2.49
FBtr0333710	CG3819	-2.49
FBtr0075048	CG3819	-2.49
FBtr0070776	CG16756	-2.49
FBtr0084028	CG10824	-2.50
FBtr0086733	Spn55B	-2.53
FBtr0086215	CG30154	-2.54
FBtr0087279	CG30090	-2.55
FBtr0306384	CG4019	-2.55
FBtr0072103	CG4019	-2.55
FBtr0072105	CG4019	-2.55
FBtr0336929	CG4019	-2.55
FBtr0072102	CG4019	-2.55
FBtr0081107	CG17322	-2.56
FBtr0081108	CG17322	-2.56
FBtr0081106	CG17322	-2.56
FBtr0345382	CG32191	-2.56
FBtr0307509	CG32191	-2.56
FBtr0332884	CG3814	-2.57
FBtr0072104	CG4019	-2.57
FBtr0083538	DNaseII	-2.57
FBtr0332885	CG3814	-2.58
FBtr0071782	CG3290	-2.58
FBtr0077063	CG10467	-2.59
FBtr0307099	CG43351	-2.59
FBtr0113597	snoRNA:Psi18S-1377b	-2.59
FBtr0306841	CG11034	-2.62
FBtr0342609	CG11034	-2.62
FBtr0344769	CG11034	-2.62
FBtr0079063	TpnC25D	-2.64
FBtr0346458	TpnC25D	-2.64
FBtr0345250	Obp83a	-2.64
FBtr0345621	CG34457	-2.67
FBtr0112763	CG34457	-2.67
FBtr0346059	CG9914	-2.67
FBtr0074240	CG9914	-2.67
FBtr0085510	CG31202	-2.67
FBtr0081105	CG17322	-2.67
FBtr0084825	CG31104	-2.68
FBtr0290287	CG12917	-2.69
FBtr0346058	CR45485	-2.69
FBtr0071745	lox2	-2.70
FBtr0086752	CG14500	-2.73
FBtr0079240	Vm26Ac	-2.74
FBtr0100081	CG34026	-2.75
FBtr0343410	CG34026	-2.75
FBtr0342931	TpnC25D	-2.76
FBtr0079275	Tig	-2.78
FBtr0343152	Tig	-2.78
FBtr0331962	CG43789	-2.81
FBtr0083967	CG15695	-2.82
FBtr0306593	CG13285	-2.82
FBtr0080162	Art8	-2.85
FBtr0077239	Npc1b	-2.85
FBtr0085305	CG9988	-2.86
FBtr0310441	CG7322	-2.89
FBtr0074654	CG7322	-2.89
FBtr0346018	CG7322	-2.89
FBtr0343681	CG42682	-2.92
FBtr0078370	CG33290	-2.92
FBtr0082726	CG7381	-2.94
FBtr0078207	CG17637	-2.95
FBtr0076314	CG32054	-2.95
FBtr0072011	yellow-d	-2.96
FBtr0076084	CG10361	-2.98
FBtr0087956	CG13155	-2.98
FBtr0301219	CG7381	-2.99
FBtr0310149	CG16965	-3.00
FBtr0071740	CG4363	-3.04
FBtr0300456	Cyp4ac2	-3.04
FBtr0342846	phm	-3.04
FBtr0074603	phm	-3.04
FBtr0331428	CG7381	-3.06
FBtr0080336	CG17211	-3.07
FBtr0331429	CG7381	-3.07
FBtr0082727	CG7381	-3.07
FBtr0332034	CG9259	-3.11
FBtr0083038	CG6912	-3.13
FBtr0332033	CG9259	-3.14
FBtr0081464	CG9259	-3.14
FBtr0075348	PGRP-SB1	-3.16
FBtr0087732	AGBE	-3.17
FBtr0088758	Mal-A3	-3.18
FBtr0085977	CG7849	-3.19
FBtr0080450	CG5945	-3.20
FBtr0334754	CG5945	-3.20
FBtr0085077	CG6295	-3.25
FBtr0076906	CG14823	-3.27
FBtr0344119	CG31091	-3.29
FBtr0076908	CG14823	-3.31
FBtr0306838	CR43304	-3.32
FBtr0073334	CG11345	-3.35
FBtr0078591	Osi24	-3.38
FBtr0078424	CG32444	-3.40
FBtr0306299	CR43242	-3.40
FBtr0077803	CG17242	-3.41
FBtr0335162	CG17242	-3.41
FBtr0087406	CG12853	-3.49
FBtr0085511	Jon99Ci	-3.57
FBtr0073073	Drs	-3.59
FBtr0080639	l(2)34Fd	-3.66
FBtr0081472	CG9246	-3.67
FBtr0347058	CR45955	-3.69
FBtr0089560	Sardh	-3.69
FBtr0074436	CG8568	-3.75
FBtr0074028	Cyp4s3	-3.75
FBtr0303833	CG42825	-3.82
FBtr0300297	Sfp24Bb	-3.84
FBtr0309041	CG31091	-3.87
FBtr0088562	CG8083	-3.88
FBtr0088561	CG8083	-3.88
FBtr0088560	CG8083	-3.88
FBtr0304879	CG43093	-3.91
FBtr0112514	CG34316	-3.98
FBtr0335233	CG31087	-4.10
FBtr0084855	CG31087	-4.10
FBtr0077025	CG5568	-4.14
FBtr0081517	CG8665	-4.16
FBtr0346232	CR45600	-4.17
FBtr0084847	tobi	-4.20
FBtr0346185	CG42807	-4.27
FBtr0303819	CG42807	-4.27
FBtr0305582	Ag5r	-4.33
FBtr0333658	Ag5r	-4.33
FBtr0310321	CG10073	-4.38
FBtr0083025	CG3984	-4.39
FBtr0330667	CG3597	-4.40
FBtr0077792	CG3597	-4.40
FBtr0086523	CG10073	-4.52
FBtr0081350	CG10659	-4.53
FBtr0088798	CG30371	-4.57
FBtr0086903	CG6484	-4.57
FBtr0083017	smp-30	-4.58
FBtr0083016	smp-30	-4.60
FBtr0336878	smp-30	-4.61
FBtr0336877	smp-30	-4.61
FBtr0088747	Mal-A2	-4.62
FBtr0073937	Ag5r	-4.64
FBtr0303828	CG42821	-4.82
FBtr0084441	CG31148	-4.85
FBtr0074392	CG18258	-4.95
FBtr0085626	CG15533	-4.95
FBtr0088707	PGRP-SC1a	-5.07
FBtr0335216	CG4757	-5.18
FBtr0082339	CG4757	-5.18
FBtr0343688	CG31832	-5.34
FBtr0073916	CG9411	-5.37
FBtr0083971	TotA	-5.37
FBtr0340492	CG15096	-5.38
FBtr0086632	CG15096	-5.53
FBtr0332756	Cpr76Bd	-5.55
FBtr0113181	Cpr76Bd	-5.55
FBtr0332755	Cpr76Bd	-5.55
FBtr0077024	Cpr65Av	-5.74
FBtr0086633	CG15096	-5.75
FBtr0071739	CG4377	-5.76
FBtr0112391	CG34198	-5.76
FBtr0088709	PGRP-SC2	-5.81
FBtr0345752	CG9466	-5.84
FBtr0079742	CG9466	-5.84
FBtr0343173	CG9572	-6.29
FBtr0077047	CG6602	-6.34
FBtr0303428	CG42782	-6.42
FBtr0347196	CG42782	-6.42
FBtr0070006	CG9572	-6.56
FBtr0303256	CG9572	-6.56
FBtr0080729	CG15263	-6.60
FBtr0072633	LysP	-6.76
FBtr0339932	Sodh-1	-6.88
FBtr0081627	Sodh-1	-6.88
FBtr0080275	Mal-B1	-6.98
FBtr0339153	CG3739	-7.34
FBtr0085007	CR31084	-7.51
FBtr0112487	CG34291	-8.02
FBtr0088748	Mal-A4	-8.65
FBtr0339748	CG13325	-8.96
FBtr0087722	CG13325	-10.00
FBtr0310455	CG43680	-10.10
FBtr0300448	Cp38	-10.30
FBtr0339997	CG8093	-10.70
FBtr0087401	CG8093	-10.70
FBtr0345931	CG13325	-11.40
FBtr0345194	CG13325	-11.40
FBtr0340230	CG9463	-12.20
FBtr0079744	CG9463	-12.50
FBtr0086475	CG15126	-13.20
FBtr0085150	CG6277	-13.70
FBtr0076810	CG7409	-14.10
FBtr0076388	CG18179	-15.80
FBtr0077128	CG10591	-17.20
FBtr0345611	CG16826	-20.90
FBtr0080464	CG16826	-20.90
FBtr0289974	CG14325	-25.20
FBtr0085151	CG6283	-25.50
FBtr0084153	fit	-29.70
FBtr0083985	TotX	-31.70
FBtr0346383	CG1678	-36.70
FBtr0077219	CG1678	-36.70
FBtr0100095	CG34040	-39.20
FBtr0335461	CG44142	-41.20
FBtr0075099	CG32198	-59.00
FBtr0077220	lcs	-63.20
FBtr0302826	CG34212	-76.20
FBtr0082900	CG33109	-77.50
FBtr0344451	CG45080	-79.10
FBtr0112405	CG34212	-116.00

3) Upregulated proteins

Count: 100 proteins

This table is related to Supplementary Table 4.

protein FC values are logged

PUP_inner_FC1.6 <- dPERK_inner_join %>% filter (prot_reg == 1)
PUP_inner_FC1.6_unq <- PUP_inner_FC1.6  %>% dplyr::select(Protein.ID, Gene.name) %>%  unique()
write.csv(PUP_inner_FC1.6, "1.6_data_output/PUP_inner_FC1.6.csv")
write.csv(PUP_inner_FC1.6_unq, "1.6_data_output/PUP_inner_FC1.6_unq.csv")

Table 3: Upregulated proteins

Transcript ID	Gene ID	Protein FC
FBtr0299943	Jabba	4.84
FBtr0100558	Hsp22	4.82
FBtr0100559	Hsp22	4.82
FBtr0087451	Cyp6a17	4.25
FBtr0345527	Cyp6a17	4.25
FBtr0302379	CG5999	3.73
FBtr0081201	Lectin-galC1	3.28
FBtr0302360	Lectin-galC1	3.28
FBtr0078098	CG11911	3.22
FBtr0078770	PEK	2.32
FBtr0347257	CG5791	1.97
FBtr0084180	CG5791	1.97
FBtr0335196	CG5791	1.97
FBtr0082569	GstD2	1.88
FBtr0070337	CG4199	1.87
FBtr0113321	Ugt86Dd	1.74
FBtr0077065	CG13295	1.64
FBtr0079925	Cyp4e3	1.57
FBtr0330618	CG6191	1.43
FBtr0112408	CG34215	1.43
FBtr0303445	CG31808	1.39
FBtr0084832	rha	1.39
FBtr0304903	Taf1	1.39
FBtr0113104	Vrp1	1.38
FBtr0077460	CG3652	1.29
FBtr0085992	bin3	1.28
FBtr0336519	bin3	1.28
FBtr0346718	bin3	1.28
FBtr0085993	bin3	1.28
FBtr0077059	Lcp65Ag2	1.27
FBtr0077058	Lcp65Ag1	1.27
FBtr0301735	CG12868	1.24
FBtr0084407	Rassf	1.24
FBtr0082195	gammaSnap2	1.24
FBtr0086774	Dgp-1	1.20
FBtr0086773	Dgp-1	1.20
FBtr0089463	asparagine-synthetase	1.20
FBtr0089055	Cyp9b2	1.19
FBtr0074255	Tob	1.19
FBtr0310446	Tob	1.19
FBtr0087105	RpLP2	1.18
FBtr0343842	CG43402	1.14
FBtr0308745	CG43402	1.14
FBtr0073544	CG1572	1.12
FBtr0073543	CG1572	1.12
FBtr0339693	CG1572	1.12
FBtr0339694	CG1572	1.12
FBtr0088020	SkpB	1.12
FBtr0113204	CG7900	1.09
FBtr0086676	GstE8	1.06
FBtr0345798	GstE8	1.06
FBtr0079424	Nuf2	1.04
FBtr0072954	Pxn	1.04
FBtr0072950	Pxn	1.04
FBtr0072951	Pxn	1.04
FBtr0072953	Pxn	1.04
FBtr0072952	Pxn	1.04
FBtr0332594	CG10543	1.04
FBtr0086673	GstE5	1.02
FBtr0072150	Fmo-1	1.02
FBtr0087601	Prosap	1.02
FBtr0337049	CG43143	1.01
FBtr0070434	CG16903	1.01
FBtr0086807	CG10912	1.00
FBtr0331535	CG10089	0.99
FBtr0085498	CG31038	0.99
FBtr0085494	CG31038	0.99
FBtr0070429	wapl	0.98
FBtr0344159	wapl	0.98
FBtr0301854	CG34423	0.97
FBtr0344361	CG45049	0.97
FBtr0078507	CG11425	0.97
FBtr0344358	CG45049	0.97
FBtr0078339	CG7632	0.96
FBtr0302646	axo	0.96
FBtr0290243	NimC3	0.96
FBtr0078868	atms	0.96
FBtr0334899	atms	0.96
FBtr0085652	Jon99Fi	0.96
FBtr0089324	Lsp2	0.93
FBtr0345352	Lsp2	0.93
FBtr0073034	CG32281	0.92
FBtr0079388	Pcp	0.91
FBtr0078752	CG2926	0.91
FBtr0331303	CG3711	0.91
FBtr0079996	CG31715	0.89
FBtr0113149	CG10274	0.88
FBtr0087455	Cyp6a8	0.88
FBtr0345816	Spn77Ba	0.87
FBtr0074841	Spn77Ba	0.87
FBtr0074842	Spn77Ba	0.87
FBtr0340576	CG5758	0.87
FBtr0081035	CG5758	0.87
FBtr0340577	CG5758	0.87
FBtr0081036	CG5758	0.87
FBtr0340575	CG5758	0.87
FBtr0081037	CG5758	0.87
FBtr0087157	CG4398	0.86
FBtr0084434	GILT3	0.86
FBtr0075944	CG10754	0.86
FBtr0084870	CG10420	0.85
FBtr0309880	dila	0.85
FBtr0079486	Uro	0.84
FBtr0084809	CG11852	0.84
FBtr0336634	Ate1	0.84
FBtr0081974	St2	0.84
FBtr0346096	St2	0.84
FBtr0087406	CG12853	0.83
FBtr0083609	mTerf5	0.83
FBtr0076567	Cpr66D	0.83
FBtr0086255	Hil	0.83
FBtr0086256	Hil	0.83
FBtr0081692	Ccp84Ab	0.82
FBtr0333095	baf	0.80
FBtr0079535	baf	0.80
FBtr0083779	CG17752	0.79
FBtr0088760	Cyp4ad1	0.78
FBtr0113248	Ire1	0.77
FBtr0089254	MED26	0.77
FBtr0089253	MED26	0.77
FBtr0086476	Obp56a	0.77
FBtr0078661	CG2017	0.76
FBtr0080592	NimC4	0.75
FBtr0076089	Tim13	0.75
FBtr0072012	yellow-d2	0.74
FBtr0111043	sns	0.73
FBtr0073499	HP5	0.73
FBtr0086699	CG10924	0.72
FBtr0346348	RpII15	0.72
FBtr0082925	RpII15	0.72
FBtr0309995	RpII15	0.72
FBtr0082648	Dtg	0.72
FBtr0083164	CG5399	0.71
FBtr0334027	CG5399	0.71
FBtr0075020	nes	0.70
FBtr0075019	nes	0.70
FBtr0075021	nes	0.70
FBtr0333351	Spn27A	0.70
FBtr0079321	Spn27A	0.70
FBtr0076421	CG3088	0.70
FBtr0080326	Pex19	0.70
FBtr0342602	Pex19	0.70

4) Downregulated proteins

Count: 145 genes

This table is related to Supplementary Table 5.

protein FC values are logged

PDOWN_inner_FC1.6 <- dPERK_inner_join %>% filter (prot_reg == -1)
PDOWN_inner_FC1.6_unq <- PDOWN_inner_FC1.6  %>% dplyr::select(Protein.ID) %>%  unique()
write.csv(PDOWN_inner_FC1.6, "1.6_data_output/PDOWN_inner_FC1.6.csv")

Table 4: Downregulated proteins

Transcript ID	Gene ID	Protein FC
FBtr0346624	bgm	-0.70
FBtr0080590	bgm	-0.70
FBtr0071670	CG10306	-0.70
FBtr0081347	vls	-0.70
FBtr0084186	CG6028	-0.71
FBtr0300956	CG30427	-0.71
FBtr0300957	CG30427	-0.71
FBtr0072414	CG30427	-0.71
FBtr0075512	CG10516	-0.71
FBtr0100081	CG34026	-0.72
FBtr0343410	CG34026	-0.72
FBtr0079507	CG13794	-0.72
FBtr0082504	CG3397	-0.72
FBtr0304888	CG43101	-0.72
FBtr0079062	Cyp28d1	-0.72
FBtr0073723	CG15717	-0.73
FBtr0344608	CG15717	-0.73
FBtr0084210	Sar1	-0.73
FBtr0084206	Sar1	-0.73
FBtr0084208	Sar1	-0.73
FBtr0084209	Sar1	-0.73
FBtr0339676	CG15717	-0.73
FBtr0086903	CG6484	-0.74
FBtr0077212	Cyp6t1	-0.74
FBtr0084879	CG5107	-0.74
FBtr0086935	CG4847	-0.74
FBtr0345706	Vha36-3	-0.74
FBtr0339401	Vha36-3	-0.74
FBtr0080101	CG17097	-0.74
FBtr0082651	Gnmt	-0.75
FBtr0089608	Dup99B	-0.75
FBtr0332091	dop	-0.75
FBtr0075562	dop	-0.75
FBtr0075207	Jon74E	-0.75
FBtr0082179	CG3940	-0.76
FBtr0344391	CG3940	-0.76
FBtr0344392	CG3940	-0.76
FBtr0345027	CG1246	-0.76
FBtr0333446	CG1246	-0.76
FBtr0072938	CG1246	-0.76
FBtr0303022	CG1246	-0.76
FBtr0100088	CG34033	-0.76
FBtr0332538	CG14606	-0.76
FBtr0081603	CG14606	-0.76
FBtr0080452	CG16820	-0.76
FBtr0083850	CG4462	-0.76
FBtr0113171	Zip71B	-0.76
FBtr0347146	Zip71B	-0.76
FBtr0071739	CG4377	-0.77
FBtr0332755	Cpr76Bd	-0.77
FBtr0079878	CG4594	-0.77
FBtr0331631	CG4594	-0.77
FBtr0300805	CG18284	-0.78
FBtr0339130	CG18284	-0.78
FBtr0112350	CG34159	-0.78
FBtr0084255	Pebp1	-0.78
FBtr0079829	CG31883	-0.78
FBtr0331223	Cpr	-0.79
FBtr0082625	CG4830	-0.79
FBtr0331224	Cpr	-0.79
FBtr0079250	Cpr	-0.79
FBtr0335171	CG15394	-0.79
FBtr0335172	CG15394	-0.79
FBtr0076758	nmo	-0.80
FBtr0076756	nmo	-0.80
FBtr0333223	nmo	-0.80
FBtr0076759	nmo	-0.80
FBtr0070006	CG9572	-0.81
FBtr0078297	CG10512	-0.81
FBtr0306695	mtd	-0.81
FBtr0334320	Mkk4	-0.81
FBtr0081892	Mkk4	-0.81
FBtr0300443	Mkk4	-0.81
FBtr0077547	CG16713	-0.82
FBtr0302944	CG9331	-0.82
FBtr0302945	CG9331	-0.82
FBtr0081420	CG9331	-0.82
FBtr0345687	CG9331	-0.82
FBtr0078089	CG11885	-0.82
FBtr0087444	hui	-0.82
FBtr0087445	hui	-0.82
FBtr0342615	CG9029	-0.83
FBtr0089105	CG1970	-0.83
FBtr0333676	CG1970	-0.83
FBtr0088158	CG30025	-0.83
FBtr0089712	CG1677	-0.83
FBtr0339819	CG1677	-0.83
FBtr0303415	CG1677	-0.83
FBtr0334297	CG9922	-0.84
FBtr0082870	CG9922	-0.84
FBtr0340319	RpL30	-0.84
FBtr0302491	RpL30	-0.84
FBtr0081181	RpL30	-0.84
FBtr0346715	Sfp35C	-0.84
FBtr0300311	Sfp35C	-0.84
FBtr0084149	CG6690	-0.84
FBtr0079076	H15	-0.85
FBtr0343225	H15	-0.85
FBtr0084847	tobi	-0.86
FBtr0072029	CG3530	-0.86
FBtr0076591	CG5804	-0.86
FBtr0074712	CG12203	-0.86
FBtr0082656	CG12279	-0.86
FBtr0071091	CG1444	-0.86
FBtr0072172	eIF-5A	-0.86
FBtr0072173	eIF-5A	-0.86
FBtr0071014	CG4607	-0.87
FBtr0071013	CG4607	-0.87
FBtr0082437	CG6908	-0.87
FBtr0290280	CG8736	-0.88
FBtr0087783	bic	-0.88
FBtr0113049	CG1701	-0.88
FBtr0332995	CG1701	-0.88
FBtr0087782	bic	-0.88
FBtr0345637	CG31872	-0.89
FBtr0080099	CG31872	-0.89
FBtr0300296	Sfp24Ba	-0.90
FBtr0074843	Spn77Bb	-0.90
FBtr0082980	Cys	-0.90
FBtr0346168	CG3106	-0.91
FBtr0071403	CG3106	-0.91
FBtr0336877	smp-30	-0.92
FBtr0081107	CG17322	-0.92
FBtr0081108	CG17322	-0.92
FBtr0081106	CG17322	-0.92
FBtr0081105	CG17322	-0.92
FBtr0080557	CG16884	-0.92
FBtr0075284	CG7724	-0.93
FBtr0085001	Ald	-0.93
FBtr0306657	Ald	-0.93
FBtr0310661	Ald	-0.93
FBtr0076810	CG7409	-0.94
FBtr0113196	CG1208	-0.94
FBtr0078848	CG14661	-0.95
FBtr0305965	CG14661	-0.95
FBtr0346813	CG14974	-0.96
FBtr0304879	CG43093	-0.97
FBtr0331816	Spn77Bc	-0.97
FBtr0078172	Spn77Bc	-0.97
FBtr0110802	CG14034	-0.97
FBtr0346459	CG14034	-0.97
FBtr0088746	Cyp4e1	-0.98
FBtr0110771	Spn75F	-0.99
FBtr0078511	CG11523	-0.99
FBtr0079624	Spn28F	-1.01
FBtr0079741	CG9468	-1.02
FBtr0075115	Met75Ca	-1.04
FBtr0082727	CG7381	-1.05
FBtr0331634	CG42367	-1.05
FBtr0344123	CG45011	-1.05
FBtr0344124	CG45011	-1.05
FBtr0088748	Mal-A4	-1.06
FBtr0079042	Rtnl1	-1.06
FBtr0332034	CG9259	-1.07
FBtr0332033	CG9259	-1.07
FBtr0081464	CG9259	-1.07
FBtr0075033	CG10424	-1.08
FBtr0076003	Est-6	-1.09
FBtr0333383	Est-6	-1.09
FBtr0088380	CG30008	-1.09
FBtr0334715	Syp	-1.12
FBtr0331931	Cyt-b5-r	-1.12
FBtr0080932	Cyt-b5-r	-1.12
FBtr0087420	Obp51a	-1.13
FBtr0306923	CG43319	-1.13
FBtr0300489	CG13585	-1.13
FBtr0300488	CG13585	-1.13
FBtr0072303	CG13585	-1.13
FBtr0072304	CG13585	-1.13
FBtr0301928	CG31624	-1.13
FBtr0343874	CG31624	-1.13
FBtr0081491	CG31624	-1.13
FBtr0305959	CG17374	-1.14
FBtr0085616	CecC	-1.14
FBtr0303818	CG42808	-1.15
FBtr0336680	St3	-1.16
FBtr0072164	PebIII	-1.18
FBtr0343340	PebIII	-1.18
FBtr0343341	PebIII	-1.18
FBtr0339932	Sodh-1	-1.19
FBtr0081627	Sodh-1	-1.19
FBtr0100353	ade3	-1.20
FBtr0083025	CG3984	-1.21
FBtr0340616	CG5162	-1.23
FBtr0074393	CG5162	-1.23
FBtr0343490	CG33228	-1.27
FBtr0301037	CG33228	-1.27
FBtr0333037	Gbs-70E	-1.30
FBtr0075724	Gbs-70E	-1.30
FBtr0301934	Sfp24Bc	-1.30
FBtr0083712	NP15.6	-1.30
FBtr0306288	CG43235	-1.33
FBtr0078207	CG17637	-1.35
FBtr0345752	CG9466	-1.35
FBtr0079742	CG9466	-1.35
FBtr0074392	CG18258	-1.55
FBtr0082248	Rrp46	-1.55
FBtr0300313	Sfp60F	-1.59
FBtr0072096	CG4091	-1.62
FBtr0072097	CG4091	-1.62
FBtr0072098	CG4091	-1.62
FBtr0072937	CG1143	-1.64
FBtr0333445	CG1143	-1.64
FBtr0088928	CG1942	-1.71
FBtr0304645	CG43061	-1.71
FBtr0303828	CG42821	-1.74
FBtr0083972	TotC	-1.77
FBtr0077803	CG17242	-1.80
FBtr0335162	CG17242	-1.80
FBtr0336732	l(2)06496	-1.94
FBtr0071985	l(2)06496	-1.94
FBtr0079499	CG7214	-2.08
FBtr0340230	CG9463	-2.11
FBtr0079744	CG9463	-2.11
FBtr0309866	CanB2	-2.59
FBtr0088930	CanB2	-2.59
FBtr0080275	Mal-B1	-2.66
FBtr0290272	CG7203	-2.83
FBtr0346499	CG7203	-2.83
FBtr0079500	Acp1	-2.87
FBtr0073937	Ag5r	-3.12
FBtr0305582	Ag5r	-3.12
FBtr0333658	Ag5r	-3.12
FBtr0082900	CG33109	-3.52
FBtr0088592	Cyp4p1	-3.90
FBtr0345611	CG16826	-5.02
FBtr0080464	CG16826	-5.02

5) Upregulated transcripts and proteins (Group 1)

Count: 27 genes

This table is related to Supplementary Table 13.

protein FC values are logged

TUP_PUP_FC1.6 <- dPERK_inner_join %>% filter (trans_reg == 1, prot_reg == 1)
TUP_PUP_FC1.6_unq <- TUP_PUP_FC1.6 %>% dplyr::select(Gene.name) %>%  unique() # for the count 
write.csv(TUP_PUP_FC1.6, "1.6_data_output/TUP_PUP_FC1.6.csv")

Table 5: Upregulated transcripts and upregulated proteins

Transcript ID	Gene ID	Transcript FC	Protein FC
FBtr0087451	Cyp6a17	117.00	4.25
FBtr0345527	Cyp6a17	117.00	4.25
FBtr0100559	Hsp22	74.60	4.82
FBtr0302379	CG5999	69.40	3.73
FBtr0100558	Hsp22	29.20	4.82
FBtr0086774	Dgp-1	25.80	1.20
FBtr0086773	Dgp-1	21.20	1.20
FBtr0078770	PEK	16.60	2.32
FBtr0084870	CG10420	8.58	0.85
FBtr0082569	GstD2	7.49	1.88
FBtr0089055	Cyp9b2	6.96	1.19
FBtr0078098	CG11911	6.96	3.22
FBtr0343842	CG43402	6.77	1.14
FBtr0308745	CG43402	6.77	1.14
FBtr0089463	asparagine-synthetase	4.30	1.20
FBtr0079486	Uro	3.73	0.84
FBtr0078339	CG7632	3.57	0.96
FBtr0113321	Ugt86Dd	3.48	1.74
FBtr0302360	Lectin-galC1	3.34	3.28
FBtr0081201	Lectin-galC1	3.26	3.28
FBtr0079925	Cyp4e3	3.22	1.57
FBtr0086676	GstE8	2.70	1.06
FBtr0345798	GstE8	2.70	1.06
FBtr0086699	CG10924	2.63	0.72
FBtr0078661	CG2017	2.60	0.76
FBtr0347257	CG5791	2.56	1.97
FBtr0084180	CG5791	2.56	1.97
FBtr0335196	CG5791	2.53	1.97
FBtr0301854	CG34423	2.40	0.97
FBtr0301735	CG12868	2.17	1.24
FBtr0113248	Ire1	2.09	0.77
FBtr0081692	Ccp84Ab	1.92	0.82
FBtr0303445	CG31808	1.84	1.39
FBtr0083779	CG17752	1.80	0.79
FBtr0088760	Cyp4ad1	1.61	0.78

6) Upregulated transcripts and no change in proteins (Group 2)

Count: 102 genes

This table is related to Supplementary Table 14.

protein FC values are logged

TUP_PZERO_FC1.6 <- dPERK_inner_join %>% filter (trans_reg == 1, prot_reg == 0, prot_FDR <= 0.05 )
TUP_PZERO_FC1.6_unq <- TUP_PZERO_FC1.6  %>% dplyr::select(Gene.name) %>%  unique()
write.csv(TUP_PZERO_FC1.6, "1.6_data_output/TUP_PZERO_FC1.6.csv")

Table 8: Upregulated transcripts and no change in proteins

Transcript ID	Gene ID	Transcript FC	Protein FC
FBtr0100655	Hsp67Bb	29.20	-0.42
FBtr0077008	ImpL3	16.30	0.33
FBtr0332066	ImpL3	16.20	0.33
FBtr0332067	ImpL3	16.10	0.33
FBtr0332065	ImpL3	16.00	0.33
FBtr0289990	CG30022	7.58	-0.23
FBtr0086749	CG10916	7.12	0.67
FBtr0332853	CG10916	7.09	0.67
FBtr0079299	Aatf	5.73	0.29
FBtr0082334	Tpc1	5.36	0.21
FBtr0336761	Nmdmc	5.34	0.59
FBtr0081996	Nmdmc	5.33	0.59
FBtr0301935	Sfp26Ad	5.32	0.44
FBtr0333233	Sfp26Ad	5.32	0.44
FBtr0082333	Tpc1	5.30	0.21
FBtr0081997	Nmdmc	4.74	0.59
FBtr0084035	CG7044	4.65	0.51
FBtr0085849	FeCH	4.60	0.33
FBtr0085850	FeCH	4.58	0.33
FBtr0080912	Ugt36Bc	4.58	0.12
FBtr0080911	Ugt36Bc	4.58	0.12
FBtr0085851	FeCH	4.57	0.33
FBtr0344850	Ugt36Bc	4.53	0.12
FBtr0089056	Cyp9b1	4.19	0.25
FBtr0344263	GstD9	3.87	0.34
FBtr0082608	GstD9	3.87	0.34
FBtr0073061	Drsl4	3.87	-0.61
FBtr0084828	CG13659	3.71	0.33
FBtr0332909	asrij	3.66	0.17
FBtr0086913	l(2)k01209	3.39	0.29
FBtr0086914	l(2)k01209	3.39	0.29
FBtr0086915	l(2)k01209	3.36	0.29
FBtr0310075	NimC1	3.24	-0.36
FBtr0343644	NimC1	3.24	-0.36
FBtr0082438	CG6834	3.21	0.16
FBtr0086675	GstE7	3.19	0.22
FBtr0073777	CG1673	3.08	0.66
FBtr0073249	ImpL2	3.07	0.16
FBtr0333569	ImpL2	3.07	0.16
FBtr0076457	aay	3.06	0.67
FBtr0076894	CG14820	3.02	0.48
FBtr0335448	Elp1	3.01	0.14
FBtr0070568	CG10802	2.96	0.15
FBtr0073250	ImpL2	2.95	0.16
FBtr0073248	ImpL2	2.94	0.16
FBtr0335480	CG17259	2.87	-0.37
FBtr0077667	CG17259	2.87	-0.37
FBtr0082570	GstD3	2.86	0.30
FBtr0077165	CG4611	2.84	0.30
FBtr0078225	CG11796	2.81	0.64
FBtr0086911	Prosalpha5	2.75	-0.44
FBtr0300127	Cyp6a20	2.74	0.11
FBtr0088834	CG1882	2.73	0.22
FBtr0345697	CG1882	2.73	0.22
FBtr0339120	CG1882	2.73	0.22
FBtr0335167	Cyp309a1	2.66	-0.46
FBtr0335166	Cyp309a1	2.66	-0.46
FBtr0080587	Cyp28a5	2.65	-0.30
FBtr0346428	l(2)37Cc	2.46	0.14
FBtr0081164	l(2)37Cc	2.46	0.14
FBtr0343672	CG33307	2.46	0.24
FBtr0080565	CG33307	2.46	0.24
FBtr0081165	l(2)37Cc	2.43	0.14
FBtr0346436	Aats-thr	2.41	0.16
FBtr0080332	Aats-thr	2.41	0.16
FBtr0079389	CG3476	2.41	-0.30
FBtr0087452	Cyp6a23	2.37	-0.61
FBtr0070146	Rbf	2.34	0.23
FBtr0339924	CG40002	2.33	0.11
FBtr0332460	NTPase	2.27	0.17
FBtr0336848	CG17107	2.25	0.38
FBtr0336847	CG17107	2.25	0.38
FBtr0080107	CG17107	2.25	0.38
FBtr0077389	CG3008	2.23	0.58
FBtr0100537	bocksbeutel	2.19	0.20
FBtr0081138	CG31793	2.18	0.39
FBtr0078216	CG5059	2.17	0.53
FBtr0086669	GstE1	2.17	0.52
FBtr0082105	bocksbeutel	2.11	0.20
FBtr0087450	Cyp6a22	2.11	-0.19
FBtr0345526	Cyp6a22	2.11	-0.19
FBtr0339983	Cyp6a22	2.11	-0.19
FBtr0334869	Orct2	2.10	0.17
FBtr0084598	Orct2	2.10	0.17
FBtr0345716	CG2658	2.07	0.14
FBtr0070502	CG2658	2.07	0.14
FBtr0078484	CG7130	2.07	0.49
FBtr0087336	eIF2B-gamma	2.06	-0.31
FBtr0301252	CG42553	2.03	0.43
FBtr0086677	GstE9	2.02	-0.58
FBtr0337048	CG3999	2.02	-0.15
FBtr0082225	CG3999	2.02	-0.15
FBtr0077586	CG3285	2.01	0.50
FBtr0339547	CG3285	2.01	0.50
FBtr0075251	CG6512	1.99	0.16
FBtr0111118	Nipped-B	1.97	0.21
FBtr0111119	Nipped-B	1.97	0.21
FBtr0088463	GstT1	1.91	0.16
FBtr0336664	Dpit47	1.89	0.22
FBtr0086146	Dpit47	1.88	0.22
FBtr0088957	Drat	1.85	0.14
FBtr0080290	CG12264	1.84	-0.35
FBtr0087560	Arc1	1.84	0.63
FBtr0301839	Ppn	1.83	0.49
FBtr0300337	Ppn	1.83	0.49
FBtr0301837	Ppn	1.83	0.49
FBtr0073908	CG1461	1.83	0.42
FBtr0332144	ltl	1.82	0.28
FBtr0301838	Ppn	1.82	0.49
FBtr0339497	CG1461	1.82	0.42
FBtr0340393	CG42306	1.80	0.23
FBtr0340392	Gint3	1.80	0.21
FBtr0081374	La	1.80	0.58
FBtr0088958	Drat	1.80	0.14
FBtr0299688	CG42306	1.79	0.23
FBtr0086654	Gint3	1.79	0.21
FBtr0299689	CG42306	1.79	0.23
FBtr0086655	Gint3	1.79	0.21
FBtr0076793	ltl	1.79	0.28
FBtr0113773	CG40002	1.79	0.11
FBtr0088923	CG2064	1.79	0.33
FBtr0082074	P58IPK	1.78	-0.14
FBtr0330137	mbf1	1.77	0.16
FBtr0080959	CG6115	1.77	0.41
FBtr0345447	CG6115	1.77	0.41
FBtr0070431	bcn92	1.77	0.28
FBtr0100653	Hsp67Bb	1.76	-0.42
FBtr0075519	mRpS31	1.75	0.30
FBtr0339539	babos	1.75	0.28
FBtr0071845	babos	1.75	0.28
FBtr0081205	CG9987	1.73	0.15
FBtr0303473	Hsp67Bb	1.72	-0.42
FBtr0079868	CG17633	1.72	0.19
FBtr0073763	Jafrac1	1.71	-0.33
FBtr0339700	Jafrac1	1.71	-0.33
FBtr0073764	Jafrac1	1.71	-0.33
FBtr0339699	Jafrac1	1.71	-0.33
FBtr0345161	Jafrac1	1.71	-0.33
FBtr0303474	Hsp67Bb	1.71	-0.42
FBtr0080837	CaBP1	1.71	-0.09
FBtr0345544	CaBP1	1.71	-0.09
FBtr0335460	CG9813	1.70	0.20
FBtr0079464	santa-maria	1.70	0.34
FBtr0346571	santa-maria	1.70	0.34
FBtr0345630	oys	1.68	0.32
FBtr0339416	oys	1.68	0.32
FBtr0088434	oys	1.68	0.32
FBtr0088901	Nop17l	1.67	0.26
FBtr0079602	CG14275	1.67	0.30
FBtr0087206	Rrp42	1.66	0.33
FBtr0088349	Ndg	1.65	0.28
FBtr0339459	Ndg	1.65	0.28
FBtr0071108	Gclc	1.65	-0.16
FBtr0340139	Gclc	1.65	-0.16
FBtr0300775	CG1319	1.65	-0.46
FBtr0080358	CG6583	1.64	0.21
FBtr0083277	mtSSB	1.64	0.27
FBtr0083711	CG14285	1.64	0.52
FBtr0076347	Dronc	1.64	0.50
FBtr0088902	Nop17l	1.63	0.26
FBtr0334792	CG3714	1.62	0.37
FBtr0331763	Alr	1.62	0.42
FBtr0082347	RpL3	1.62	-0.21
FBtr0071107	Gclc	1.61	-0.16
FBtr0340138	Gclc	1.61	-0.16
FBtr0072963	CG16758	1.61	-0.22
FBtr0074798	Nup205	1.61	0.16
FBtr0075338	Rh4	1.60	0.56
FBtr0075965	CG4069	1.60	0.16

7) Upregulated transcripts and no change/downregulation in proteins

Count: 107 genes

protein FC values are logged

TUP_PZERO_DOWN_FC1.6 <- dPERK_inner_join %>% filter (trans_reg == 1, prot_reg <= 0, prot_FDR <= 0.05 )
TUP_PZERO_DOWN_FC1.6_unq <- TUP_PZERO_DOWN_FC1.6  %>% dplyr::select(Gene.name) %>%  unique()
write.csv(TUP_PZERO_DOWN_FC1.6, "1.6_data_output/TUP_PZERO_DOWN_FC1.6.csv")

Table 9: Upregulated transcripts and no change/downregulation in proteins

Transcript ID	Gene ID	Transcript FC	Protein FC
FBtr0100655	Hsp67Bb	29.20	-0.42
FBtr0077008	ImpL3	16.30	0.33
FBtr0332066	ImpL3	16.20	0.33
FBtr0332067	ImpL3	16.10	0.33
FBtr0332065	ImpL3	16.00	0.33
FBtr0289990	CG30022	7.58	-0.23
FBtr0086749	CG10916	7.12	0.67
FBtr0332853	CG10916	7.09	0.67
FBtr0079299	Aatf	5.73	0.29
FBtr0082334	Tpc1	5.36	0.21
FBtr0336761	Nmdmc	5.34	0.59
FBtr0081996	Nmdmc	5.33	0.59
FBtr0301935	Sfp26Ad	5.32	0.44
FBtr0333233	Sfp26Ad	5.32	0.44
FBtr0082333	Tpc1	5.30	0.21
FBtr0081997	Nmdmc	4.74	0.59
FBtr0084035	CG7044	4.65	0.51
FBtr0085849	FeCH	4.60	0.33
FBtr0085850	FeCH	4.58	0.33
FBtr0080912	Ugt36Bc	4.58	0.12
FBtr0080911	Ugt36Bc	4.58	0.12
FBtr0085851	FeCH	4.57	0.33
FBtr0344850	Ugt36Bc	4.53	0.12
FBtr0100353	ade3	4.45	-1.20
FBtr0089056	Cyp9b1	4.19	0.25
FBtr0344263	GstD9	3.87	0.34
FBtr0082608	GstD9	3.87	0.34
FBtr0073061	Drsl4	3.87	-0.61
FBtr0084828	CG13659	3.71	0.33
FBtr0332909	asrij	3.66	0.17
FBtr0086913	l(2)k01209	3.39	0.29
FBtr0086914	l(2)k01209	3.39	0.29
FBtr0086915	l(2)k01209	3.36	0.29
FBtr0310075	NimC1	3.24	-0.36
FBtr0343644	NimC1	3.24	-0.36
FBtr0082438	CG6834	3.21	0.16
FBtr0086675	GstE7	3.19	0.22
FBtr0306923	CG43319	3.12	-1.13
FBtr0073777	CG1673	3.08	0.66
FBtr0073249	ImpL2	3.07	0.16
FBtr0333569	ImpL2	3.07	0.16
FBtr0076457	aay	3.06	0.67
FBtr0076894	CG14820	3.02	0.48
FBtr0335448	Elp1	3.01	0.14
FBtr0070568	CG10802	2.96	0.15
FBtr0073250	ImpL2	2.95	0.16
FBtr0073248	ImpL2	2.94	0.16
FBtr0077547	CG16713	2.87	-0.82
FBtr0335480	CG17259	2.87	-0.37
FBtr0077667	CG17259	2.87	-0.37
FBtr0082570	GstD3	2.86	0.30
FBtr0077165	CG4611	2.84	0.30
FBtr0078225	CG11796	2.81	0.64
FBtr0086911	Prosalpha5	2.75	-0.44
FBtr0300127	Cyp6a20	2.74	0.11
FBtr0088834	CG1882	2.73	0.22
FBtr0345697	CG1882	2.73	0.22
FBtr0339120	CG1882	2.73	0.22
FBtr0335167	Cyp309a1	2.66	-0.46
FBtr0335166	Cyp309a1	2.66	-0.46
FBtr0080587	Cyp28a5	2.65	-0.30
FBtr0088928	CG1942	2.54	-1.71
FBtr0346428	l(2)37Cc	2.46	0.14
FBtr0081164	l(2)37Cc	2.46	0.14
FBtr0343672	CG33307	2.46	0.24
FBtr0080565	CG33307	2.46	0.24
FBtr0081165	l(2)37Cc	2.43	0.14
FBtr0346436	Aats-thr	2.41	0.16
FBtr0080332	Aats-thr	2.41	0.16
FBtr0079389	CG3476	2.41	-0.30
FBtr0087452	Cyp6a23	2.37	-0.61
FBtr0070146	Rbf	2.34	0.23
FBtr0339924	CG40002	2.33	0.11
FBtr0332460	NTPase	2.27	0.17
FBtr0336848	CG17107	2.25	0.38
FBtr0336847	CG17107	2.25	0.38
FBtr0080107	CG17107	2.25	0.38
FBtr0077389	CG3008	2.23	0.58
FBtr0100537	bocksbeutel	2.19	0.20
FBtr0081138	CG31793	2.18	0.39
FBtr0078216	CG5059	2.17	0.53
FBtr0086669	GstE1	2.17	0.52
FBtr0082105	bocksbeutel	2.11	0.20
FBtr0087450	Cyp6a22	2.11	-0.19
FBtr0345526	Cyp6a22	2.11	-0.19
FBtr0339983	Cyp6a22	2.11	-0.19
FBtr0334869	Orct2	2.10	0.17
FBtr0084598	Orct2	2.10	0.17
FBtr0345716	CG2658	2.07	0.14
FBtr0070502	CG2658	2.07	0.14
FBtr0078484	CG7130	2.07	0.49
FBtr0087336	eIF2B-gamma	2.06	-0.31
FBtr0301252	CG42553	2.03	0.43
FBtr0086677	GstE9	2.02	-0.58
FBtr0337048	CG3999	2.02	-0.15
FBtr0082225	CG3999	2.02	-0.15
FBtr0077586	CG3285	2.01	0.50
FBtr0339547	CG3285	2.01	0.50
FBtr0075251	CG6512	1.99	0.16
FBtr0111118	Nipped-B	1.97	0.21
FBtr0111119	Nipped-B	1.97	0.21
FBtr0088463	GstT1	1.91	0.16
FBtr0336664	Dpit47	1.89	0.22
FBtr0086146	Dpit47	1.88	0.22
FBtr0088957	Drat	1.85	0.14
FBtr0080290	CG12264	1.84	-0.35
FBtr0087560	Arc1	1.84	0.63
FBtr0301839	Ppn	1.83	0.49
FBtr0300337	Ppn	1.83	0.49
FBtr0301837	Ppn	1.83	0.49
FBtr0073908	CG1461	1.83	0.42
FBtr0332144	ltl	1.82	0.28
FBtr0301838	Ppn	1.82	0.49
FBtr0339497	CG1461	1.82	0.42
FBtr0340393	CG42306	1.80	0.23
FBtr0340392	Gint3	1.80	0.21
FBtr0081374	La	1.80	0.58
FBtr0088958	Drat	1.80	0.14
FBtr0299688	CG42306	1.79	0.23
FBtr0086654	Gint3	1.79	0.21
FBtr0299689	CG42306	1.79	0.23
FBtr0086655	Gint3	1.79	0.21
FBtr0076793	ltl	1.79	0.28
FBtr0113773	CG40002	1.79	0.11
FBtr0088923	CG2064	1.79	0.33
FBtr0082074	P58IPK	1.78	-0.14
FBtr0330137	mbf1	1.77	0.16
FBtr0080959	CG6115	1.77	0.41
FBtr0345447	CG6115	1.77	0.41
FBtr0070431	bcn92	1.77	0.28
FBtr0100653	Hsp67Bb	1.76	-0.42
FBtr0075519	mRpS31	1.75	0.30
FBtr0339539	babos	1.75	0.28
FBtr0071845	babos	1.75	0.28
FBtr0081205	CG9987	1.73	0.15
FBtr0303473	Hsp67Bb	1.72	-0.42
FBtr0079868	CG17633	1.72	0.19
FBtr0073763	Jafrac1	1.71	-0.33
FBtr0339700	Jafrac1	1.71	-0.33
FBtr0073764	Jafrac1	1.71	-0.33
FBtr0339699	Jafrac1	1.71	-0.33
FBtr0345161	Jafrac1	1.71	-0.33
FBtr0303474	Hsp67Bb	1.71	-0.42
FBtr0080837	CaBP1	1.71	-0.09
FBtr0345544	CaBP1	1.71	-0.09
FBtr0335460	CG9813	1.70	0.20
FBtr0079464	santa-maria	1.70	0.34
FBtr0346571	santa-maria	1.70	0.34
FBtr0345630	oys	1.68	0.32
FBtr0339416	oys	1.68	0.32
FBtr0088434	oys	1.68	0.32
FBtr0088901	Nop17l	1.67	0.26
FBtr0079602	CG14275	1.67	0.30
FBtr0087206	Rrp42	1.66	0.33
FBtr0088349	Ndg	1.65	0.28
FBtr0339459	Ndg	1.65	0.28
FBtr0071108	Gclc	1.65	-0.16
FBtr0340139	Gclc	1.65	-0.16
FBtr0300775	CG1319	1.65	-0.46
FBtr0080358	CG6583	1.64	0.21
FBtr0083277	mtSSB	1.64	0.27
FBtr0083711	CG14285	1.64	0.52
FBtr0076347	Dronc	1.64	0.50
FBtr0088902	Nop17l	1.63	0.26
FBtr0088592	Cyp4p1	1.63	-3.90
FBtr0334792	CG3714	1.62	0.37
FBtr0331763	Alr	1.62	0.42
FBtr0082347	RpL3	1.62	-0.21
FBtr0071107	Gclc	1.61	-0.16
FBtr0340138	Gclc	1.61	-0.16
FBtr0072963	CG16758	1.61	-0.22
FBtr0074798	Nup205	1.61	0.16
FBtr0075338	Rh4	1.60	0.56
FBtr0075965	CG4069	1.60	0.16

8) Downregulated transcripts & proteins (group 3)

Count: 75 transcripts, matching to 51 genes

This table is related to Supplementary Table 15.

TDOWN_PDOWN_FC1.6 <- dPERK_full_join %>% filter (trans_reg == -1, prot_reg == -1)
TDOWN_PDOWN_FC1.6_unq <- TDOWN_PDOWN_FC1.6  %>% dplyr::select(Gene.name) %>%  unique()
write.csv(TDOWN_PDOWN_FC1.6 , "1.6_data_output/TDOWN_PDOWN_FC1.6 .csv")
write.csv(TDOWN_PDOWN_FC1.6_unq, "1.6_data_output/TDOWN_PDOWN_FC1.6_unq.csv")

Table 10: Downregulated transcripts and proteins

Transcript ID	Gene ID	Transcript FC	Protein FC
FBtr0089608	Dup99B	-1.63	-0.75
FBtr0100088	CG34033	-1.65	-0.76
FBtr0082625	CG4830	-1.66	-0.79
FBtr0346624	bgm	-1.70	-0.70
FBtr0080590	bgm	-1.70	-0.70
FBtr0113196	CG1208	-1.71	-0.94
FBtr0110771	Spn75F	-1.74	-0.99
FBtr0087420	Obp51a	-1.75	-1.13
FBtr0303818	CG42808	-1.79	-1.15
FBtr0086935	CG4847	-1.80	-0.74
FBtr0331816	Spn77Bc	-1.85	-0.97
FBtr0078172	Spn77Bc	-1.85	-0.97
FBtr0333446	CG1246	-1.86	-0.76
FBtr0072938	CG1246	-1.86	-0.76
FBtr0303022	CG1246	-1.86	-0.76
FBtr0078297	CG10512	-1.87	-0.81
FBtr0345027	CG1246	-1.87	-0.76
FBtr0336680	St3	-1.95	-1.16
FBtr0074843	Spn77Bb	-2.04	-0.90
FBtr0084255	Pebp1	-2.11	-0.78
FBtr0082179	CG3940	-2.14	-0.76
FBtr0344391	CG3940	-2.14	-0.76
FBtr0344392	CG3940	-2.14	-0.76
FBtr0300805	CG18284	-2.15	-0.78
FBtr0339130	CG18284	-2.15	-0.78
FBtr0305959	CG17374	-2.17	-1.14
FBtr0300296	Sfp24Ba	-2.25	-0.90
FBtr0078848	CG14661	-2.29	-0.95
FBtr0305965	CG14661	-2.29	-0.95
FBtr0304645	CG43061	-2.32	-1.71
FBtr0076003	Est-6	-2.33	-1.09
FBtr0333383	Est-6	-2.33	-1.09
FBtr0079741	CG9468	-2.35	-1.02
FBtr0340616	CG5162	-2.36	-1.23
FBtr0074393	CG5162	-2.36	-1.23
FBtr0077212	Cyp6t1	-2.36	-0.74
FBtr0082651	Gnmt	-2.37	-0.75
FBtr0081107	CG17322	-2.56	-0.92
FBtr0081108	CG17322	-2.56	-0.92
FBtr0081106	CG17322	-2.56	-0.92
FBtr0081105	CG17322	-2.67	-0.92
FBtr0100081	CG34026	-2.75	-0.72
FBtr0343410	CG34026	-2.75	-0.72
FBtr0078207	CG17637	-2.95	-1.35
FBtr0082727	CG7381	-3.07	-1.05
FBtr0332034	CG9259	-3.11	-1.07
FBtr0332033	CG9259	-3.14	-1.07
FBtr0081464	CG9259	-3.14	-1.07
FBtr0077803	CG17242	-3.41	-1.80
FBtr0335162	CG17242	-3.41	-1.80
FBtr0304879	CG43093	-3.91	-0.97
FBtr0084847	tobi	-4.20	-0.86
FBtr0305582	Ag5r	-4.33	-3.12
FBtr0333658	Ag5r	-4.33	-3.12
FBtr0083025	CG3984	-4.39	-1.21
FBtr0086903	CG6484	-4.57	-0.74
FBtr0336877	smp-30	-4.61	-0.92
FBtr0073937	Ag5r	-4.64	-3.12
FBtr0303828	CG42821	-4.82	-1.74
FBtr0074392	CG18258	-4.95	-1.55
FBtr0332755	Cpr76Bd	-5.55	-0.77
FBtr0071739	CG4377	-5.76	-0.77
FBtr0345752	CG9466	-5.84	-1.35
FBtr0079742	CG9466	-5.84	-1.35
FBtr0070006	CG9572	-6.56	-0.81
FBtr0339932	Sodh-1	-6.88	-1.19
FBtr0081627	Sodh-1	-6.88	-1.19
FBtr0080275	Mal-B1	-6.98	-2.66
FBtr0088748	Mal-A4	-8.65	-1.06
FBtr0340230	CG9463	-12.20	-2.11
FBtr0079744	CG9463	-12.50	-2.11
FBtr0076810	CG7409	-14.10	-0.94
FBtr0345611	CG16826	-20.90	-5.02
FBtr0080464	CG16826	-20.90	-5.02
FBtr0082900	CG33109	-77.50	-3.52

iRegulon: Upstream analysis

I will be using iRegulon, a Cytoscape app for upstream analysis. Before submitting IDs, I converted the transcript IDs by FlyBase converter into most recent gene names. This conversion allows optimal results in iRegulon (most recognised IDs).

Reference: Janky R, Verfaillie A, Imrichová H, Van de Sande B, Standaert L, Christiaens V, et al. (2014) iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections. PLoS Comput Biol 10(7): e1003731. https://doi.org/10.1371/journal.pcbi.1003731

iRegulon results: Upregulated transcripts

This figure is related to Figure 2 and Supplementary Table 6.

# Load the transcription factor table 
iRegulon_TUP_FC1.6 <- read.csv("Analysis/iRegulon_short_TUP_full_FC1.6_unq.csv",  header = TRUE, sep = ",") 

## Warning in read.table(file = file, header = header, sep = sep, quote =
## quote, : incomplete final line found by readTableHeader on 'Analysis/
## iRegulon_short_TUP_full_FC1.6_unq.csv'

iRegulon_TUP_FC1.6 <- as.data.frame(iRegulon_TUP_FC1.6)
iRegulon_TUP_FC1.6$NES <- as.numeric(iRegulon_TUP_FC1.6$NES)
iRegulon_TUP_FC1.6 <- iRegulon_TUP_FC1.6 %>% arrange(desc(NES)) # Arrage the data how you want it in the plot 
iRegulon_TUP_FC1.6  <- iRegulon_TUP_FC1.6 %>% mutate(TF = fct_reorder(TF, (NES))) # Lock in factor level order

# Make the plot 
iRegulon_TUP_FC1.6_plot <- ggplot(iRegulon_TUP_FC1.6, aes(x = NES, y = TF, fill=TF)) + geom_bar(stat="identity", width=0.7 ) + scale_fill_brewer(palette="RdBu") +  theme_classic() + ylab(NULL) + xlab("NES score") + theme(axis.title.x = element_text(vjust=-0.5))  + theme(axis.text.y = element_text(face = "plain", colour = "black"))  + theme(axis.ticks = element_blank()) + theme(legend.position="none", text = element_text(size=25, color = "black")) + geom_text(aes(label=Targets ), size=6, nudge_x = .4, color = "black" )  + scale_x_continuous(expand = c(0, 0), limits = c(0, 9), breaks = scales::pretty_breaks(n = 6))  

iRegulon_TUP_FC1.6_plot

# Save 
ggsave("1.6_figure_output/iRegulon_TUP_FC1.6_plot.pdf", scale = 1, dpi = 320,  limitsize = TRUE)

## Saving 7 x 5 in image

iRegulon results:Upregulated proteins

This figure is related to Figure 2 and Supplementary Table 7.

iRegulon_PUP_FC1.6 <- read.csv("Analysis/iRegulon_short_PUP_inner_FC1.6_unq.csv",  header = TRUE, sep = ",") 

## Warning in read.table(file = file, header = header, sep = sep, quote =
## quote, : incomplete final line found by readTableHeader on 'Analysis/
## iRegulon_short_PUP_inner_FC1.6_unq.csv'

iRegulon_PUP_FC1.6 <- as.data.frame(iRegulon_PUP_FC1.6)
iRegulon_PUP_FC1.6$NES <- as.numeric(iRegulon_PUP_FC1.6$NES)
iRegulon_PUP_FC1.6 <- iRegulon_PUP_FC1.6 %>% arrange(desc(NES)) # arrage the data how you want it in the plot 
iRegulon_PUP_FC1.6  <- iRegulon_PUP_FC1.6 %>% mutate(TF = fct_reorder(TF, (NES))) # lock in factor level order

iRegulon_PUP_FC1.6_plot <- ggplot(iRegulon_PUP_FC1.6, aes(x = NES, y = TF, fill=TF)) + geom_bar(stat="identity", width=0.7 ) + scale_fill_brewer(palette="RdBu") +  theme_classic() + ylab(NULL) + xlab("NES score") + theme(axis.title.x = element_text(vjust=-0.5))  + theme(axis.text.y = element_text(face = "plain", colour = "black"))  + theme(axis.ticks = element_blank()) + theme(legend.position="none", text = element_text(size=25, color = "black")) + geom_text(aes(label=Targets ), size=6, nudge_x = .4, color = "black" )  + scale_x_continuous(expand = c(0, 0), limits = c(0, 5), breaks = scales::pretty_breaks(n = 6))  

iRegulon_PUP_FC1.6_plot

ggsave("1.6_figure_output/iRegulon_PUP_FC1.6_plot.pdf", scale = 1, dpi = 320,  limitsize = TRUE)

## Saving 7 x 5 in image

 

ClueGo: Pathway enrichment analysis

I will be using ClueGO analysis, a Cytoscape application for pathway enrichment analysis. I will use protein Uniprot IDs or Gene names as identifiers.

Reference: Bindea G, Mlecnik B, Hackl H, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091-1093. doi:10.1093/bioinformatics/btp101

ClueGo results: Upregulated transcripts

This table is related to Supplementary Table 8.

# Import table into R 
ClueGOResultTable_TUP_1.6 <- read.csv("Analysis/ClueGOResultTable_TUP_full_1.6.csv",  header = TRUE, sep = ",")
# Arrange based on adjucted Term p-value
ClueGOResultTable_TUP_1.6 = ClueGOResultTable_TUP_1.6 %>% arrange(Term_PValue_Corrected_with_Bonferroni_step_down)

Table 11: ClueGO Results Table: Upregulated transcripts

GO ID	GO Term	Ontology	Term P-value corrected	Group P-value corrected	% Associated Genes	No. Genes	Associated Genes
GO:0006399	tRNA metabolic process	GO_BP	0.0000000	0	18.18	26	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG10189, CG10802, CG12264, CG17259, CG18596, CG33123, CG33785, CG33786, CG4611, CG6353, CG9987, Elp1, Elp2, JhI-1, MetRS, Rrp42
GO:0004812	aminoacyl-tRNA ligase activity	GO_MF	0.0000000	0	35.90	14	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG10802, CG17259, CG33123, MetRS
GO:0006418	tRNA aminoacylation for protein translation	GO_BP	0.0000000	0	35.90	14	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG10802, CG17259, CG33123, MetRS
GO:0004812	aminoacyl-tRNA ligase activity	GO_BP	0.0000000	0	35.90	14	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG10802, CG17259, CG33123, MetRS
GO:0006418	tRNA aminoacylation for protein translation	GO_BP	0.0000000	0	35.90	14	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG10802, CG17259, CG33123, MetRS
GO:0020037	heme binding	GO_MF	0.0000001	0	16.11	24	CG10337, CG13077, Cyp12d1-d, Cyp12d1-p, Cyp28a5, Cyp309a1, Cyp4ad1, Cyp4e3, Cyp4p1, Cyp4p2, Cyp6a14, Cyp6a17, Cyp6a2, Cyp6a20, Cyp6a21, Cyp6a22, Cyp6a23, Cyp6a9, Cyp6d2, Cyp6d4, Cyp9b1, Cyp9b2, Cyp9c1, Cyt-b5
KEGG:00982	Drug metabolism	KEGG	0.0000002	0	23.53	16	CG10178, CG5724, CG5999, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, Ugt36Ba, Ugt36Bc, Ugt86Dd
KEGG:00980	Metabolism of xenobiotics by cytochrome P450	KEGG	0.0000003	0	23.19	16	CG10178, CG5724, CG5999, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, Ugt36Ba, Ugt36Bc, Ugt86Dd
GO:0005506	iron ion binding	GO_MF	0.0000020	0	14.11	23	CG30022, CG32500, Cyp12d1-d, Cyp12d1-p, Cyp28a5, Cyp309a1, Cyp4ad1, Cyp4e3, Cyp4p1, Cyp4p2, Cyp6a14, Cyp6a17, Cyp6a2, Cyp6a20, Cyp6a21, Cyp6a22, Cyp6a23, Cyp6a9, Cyp6d2, Cyp6d4, Cyp9b1, Cyp9b2, Cyp9c1
GO:0034660	ncRNA metabolic process	GO_BP	0.0000038	0	9.89	35	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG10189, CG10802, CG12264, CG14906, CG17259, CG1785, CG18596, CG3008, CG33123, CG33785, CG33786, CG4611, CG6353, CG6686, CG9253, CG9987, Dbp45A, Elp1, Elp2, Gasz, JhI-1, MetRS, Rrp42, mtTFB1, tx
KEGG:00983	Drug metabolism	KEGG	0.0000063	0	17.71	17	CG10178, CG5724, CG5999, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, Ugt36Ba, Ugt36Bc, Ugt86Dd, l(2)k01209
GO:0006749	glutathione metabolic process	GO_BP	0.0000083	0	23.64	13	CG30022, Gclc, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, MetRS
GO:0006520	cellular amino acid metabolic process	GO_BP	0.0000093	0	12.57	24	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, AsnS, CG10802, CG11796, CG1461, CG1673, CG17259, CG33123, CG3999, CG6428, CG9674, MetRS, Odc1, Ppn, aay
GO:0006450	regulation of translational fidelity	GO_BP	0.0000099	0	47.06	8	Aats-ala, Aats-ile, Aats-thr, Aats-val, CG10802, CG33123, CG33785, CG33786
R-DME:72731	Recycling of eIF2:GDP	REACTOME	0.0000126	0	75.00	6	eIF-2alpha, eIF-2beta, eIF2B-alpha, eIF2B-delta, eIF2B-epsilon, eIF2B-gamma
KEGG:00970	Aminoacyl-tRNA biosynthesis	KEGG	0.0000562	0	20.31	13	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG17259, CG33123, MetRS
GO:0140101	catalytic activity, acting on a tRNA	GO_BP	0.0000616	0	16.16	16	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG10802, CG17259, CG17327, CG18596, CG33123, MetRS
GO:0005851	eukaryotic translation initiation factor 2B complex	GO_CC	0.0000829	0	83.33	5	eIF-2alpha, eIF2B-alpha, eIF2B-delta, eIF2B-epsilon, eIF2B-gamma
GO:0006518	peptide metabolic process	GO_BP	0.0000944	0	7.50	46	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG10802, CG17259, CG2017, CG30022, CG33123, CG7791, Dgp-1, Gclc, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, HBS1, JhI-1, MetRS, P32, PEK, RpL3, Thor, brat, eIF-2alpha, eIF-2beta, eIF2B-alpha, eIF2B-delta, eIF2B-epsilon, eIF2B-gamma, eIF2D, mRpS31, mtTFB1, rho
GO:0006518	peptide metabolic process	GO_BP	0.0000944	0	7.50	46	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, CG10802, CG17259, CG2017, CG30022, CG33123, CG7791, Dgp-1, Gclc, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, HBS1, JhI-1, MetRS, P32, PEK, RpL3, Thor, brat, eIF-2alpha, eIF-2beta, eIF2B-alpha, eIF2B-delta, eIF2B-epsilon, eIF2B-gamma, eIF2D, mRpS31, mtTFB1, rho
GO:0043603	cellular amide metabolic process	GO_BP	0.0001904	0	7.04	50	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, AsnS, CG10802, CG17259, CG2017, CG30022, CG33123, CG7791, CG8303, Dgp-1, Gclc, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, HBS1, Hmgs, JhI-1, MetRS, P32, PEK, RpL3, Thor, Uro, brat, eIF-2alpha, eIF-2beta, eIF2B-alpha, eIF2B-delta, eIF2B-epsilon, eIF2B-gamma, eIF2D, mRpS31, mtTFB1, rho
GO:0004364	glutathione transferase activity	GO_MF	0.0001940	0	25.00	10	GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1
GO:0006575	cellular modified amino acid metabolic process	GO_BP	0.0002006	0	15.79	15	CG30022, CG34423, Gclc, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, MetRS, Nmdmc
GO:0002161	aminoacyl-tRNA editing activity	GO_BP	0.0003630	0	50.00	6	Aats-ala, Aats-ile, Aats-thr, Aats-val, CG10802, CG33123
GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	GO_MF	0.0005750	0	18.18	12	CG10778, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, qm
GO:0098827	endoplasmic reticulum subcompartment	GO_CC	0.0006440	0	8.25	33	CG11796, CG13887, CG1942, CG42508, CG8311, Cyp28a5, Cyp309a1, Cyp4ad1, Cyp4e3, Cyp4p1, Cyp4p2, Cyp6a14, Cyp6a17, Cyp6a2, Cyp6a20, Cyp6a21, Cyp6a22, Cyp6a23, Cyp6a9, Cyp6d2, Cyp6d4, Cyp9b1, Cyp9b2, Cyp9c1, Cyt-b5, Ero1L, Ire1, PEK, SREBP, Sec22, Vti1b, meigo, p115
GO:0005737	cytoplasm	GO_CC	0.0010501	0	4.31	212	ALiX, Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, Alr, Arc1, AsnS, Atg1, Atg14, Atg17, Bet1, CD98hc, CG10189, CG10336, CG10420, CG10638, CG10778, CG10924, CG11796, CG12264, CG12379, CG12766, CG13887, CG15483, CG1673, CG16758, CG17259, CG17327, CG17544, CG17904, CG1942, CG2658, CG30022, CG3008, CG32280, CG32500, CG33123, CG33156, CG33785, CG33786, CG34423, CG3476, CG3714, CG3740, CG3999, CG42496, CG42508, CG43319, CG43320, CG44194, CG4611, CG5059, CG5323, CG5382, CG5521, CG5805, CG6512, CG6583, CG6769, CG7083, CG7272, CG7394, CG7791, CG8303, CG8311, CG8728, CG9773, CaBP1, Ccdc56, Cyp12d1-d, Cyp12d1-p, Cyp28a5, Cyp309a1, Cyp4ad1, Cyp4e3, Cyp4p1, Cyp4p2, Cyp6a14, Cyp6a17, Cyp6a2, Cyp6a20, Cyp6a21, Cyp6a22, Cyp6a23, Cyp6a9, Cyp6d2, Cyp6d4, Cyp9b1, Cyp9b2, Cyp9c1, Cyt-b5, DCTN6-p27, Dpit47, Dronc, Elp1, Elp2, Ero1L, Fdx1, Fdx2, FeCH, Gadd45, Gasz, Gclc, Gcn5, Gint3, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, HBS1, Hsp22, Hsp70Ba, ImpL3, Ire1, Jafrac1, JhI-1, Kr-h2, Leash, MFS3, MetRS, ND-AGGG, NTPase, Nmd3, Nmdmc, Nop17l, Nsf2, Nxt1, Odc1, P32, P58IPK, PEK, POSH, Pbgs, Pgam5, Phb2, Ppcdc, Ppn, Prosalpha5, Qtzl, REPTOR, Ranbp21, Rbf, RpL3, Rrp42, SREBP, Sec22, Shawn, Thor, Tim17b2, Tpc1, Traf4, Tspo, Uro, Vti1b, Xport, aay, ade3, asrij, bcn92, bor, brat, c11.1, cactin, daw, dia, eIF-2alpha, eIF-2beta, eIF2B-alpha, eIF2B-delta, eIF2B-epsilon, eIF2B-gamma, eIF2D, f, galectin, gt, gukh, l(2)37Cc, l(2)k01209, lft, lig3, mRpS31, mal, mbf1, meigo, mib1, mtSSB, mtTFB1, olf413, p115, rempA, rho, rpr, santa-maria, scf, sima, trbl, tx, unk, wus
R-DME:8949664	Processing of SMDT1	REACTOME	0.0015576	0	55.56	5	CG2658, CG6512, CG8728, Phb2, l(2)37Cc
GO:0006790	sulfur compound metabolic process	GO_BP	0.0016522	0	10.70	20	CG12264, CG17904, CG30022, CG32500, CG8303, Gclc, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, Hmgs, MetRS, Qtzl, bcn92
GO:0046914	transition metal ion binding	GO_MF	0.0024232	0	6.49	49	Aats-ala, B-H2, CG10916, CG10924, CG11710, CG12379, CG14820, CG17633, CG2658, CG30022, CG31457, CG32500, CG33785, CG42496, CG5382, CG6512, CG6769, CG8089, Cyp12d1-d, Cyp12d1-p, Cyp28a5, Cyp309a1, Cyp4ad1, Cyp4e3, Cyp4p1, Cyp4p2, Cyp6a14, Cyp6a17, Cyp6a2, Cyp6a20, Cyp6a21, Cyp6a22, Cyp6a23, Cyp6a9, Cyp6d2, Cyp6d4, Cyp9b1, Cyp9b2, Cyp9c1, POSH, Pbgs, Rpb12, Traf4, az2, brat, mal, mib1, olf413, unk
KEGG:00480	Glutathione metabolism	KEGG	0.0039490	0	15.19	12	Gclc, GstD2, GstD3, GstD9, GstE1, GstE11, GstE6, GstE7, GstE8, GstE9, GstT1, Odc1
GO:0048280	vesicle fusion with Golgi apparatus	GO_BP	0.0058077	0	66.67	4	Bet1, Sec22, Vti1b, p115
KEGG:00860	Porphyrin and chlorophyll metabolism	KEGG	0.0060275	0	19.57	9	Aats-glupro, CG10178, CG5724, CG5999, FeCH, Pbgs, Ugt36Ba, Ugt36Bc, Ugt86Dd
R-DME:196849	Metabolism of water-soluble vitamins and cofactors	REACTOME	0.0060836	0	12.73	14	CG11912, CG12264, CG17751, CG17752, CG3714, CG4407, CG7084, CG7342, CG7720, Cyt-b5, Nmdmc, Ppcdc, Tpc1, mal
GO:0006082	organic acid metabolic process	GO_BP	0.0064924	0	7.49	32	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, AsnS, CG10802, CG10924, CG11796, CG13334, CG1461, CG1673, CG17259, CG17544, CG33123, CG3999, CG5805, CG6428, CG9674, ImpL3, MetRS, Nmdmc, Odc1, Ppn, SREBP, Uro, aay
R-DME:8949215	Mitochondrial calcium ion transport	REACTOME	0.0138688	0	38.46	5	CG2658, CG6512, CG8728, Phb2, l(2)37Cc
GO:0005739	mitochondrion	GO_CC	0.0158553	0	5.80	55	Aats-ala, Aats-gly, Aats-his, Aats-thr, Alr, CG10924, CG12264, CG12379, CG1673, CG17327, CG2658, CG30022, CG32500, CG34423, CG3476, CG3740, CG3999, CG42496, CG44194, CG4611, CG5059, CG5805, CG6512, CG7394, CG7791, CG8728, Ccdc56, Cyp12d1-d, Cyp12d1-p, Fdx1, Fdx2, FeCH, Gasz, Hsp22, JhI-1, ND-AGGG, Nmdmc, P32, Pgam5, Phb2, Ppn, Qtzl, Shawn, Tim17b2, Tpc1, Tspo, bcn92, bor, l(2)37Cc, lig3, mRpS31, mal, mtSSB, mtTFB1, rpr
GO:0019752	carboxylic acid metabolic process	GO_BP	0.0198820	0	7.28	30	Aats-ala, Aats-asn, Aats-asp, Aats-glupro, Aats-gly, Aats-his, Aats-ile, Aats-thr, Aats-trp, Aats-val, AsnS, CG10802, CG10924, CG11796, CG13334, CG1461, CG1673, CG17259, CG17544, CG33123, CG3999, CG6428, CG9674, ImpL3, MetRS, Nmdmc, Odc1, Ppn, SREBP, aay
GO:0005783	endoplasmic reticulum	GO_CC	0.0204861	0	6.32	42	CG10420, CG10778, CG11796, CG13887, CG1942, CG3740, CG42508, CG8311, CaBP1, Cyp28a5, Cyp309a1, Cyp4ad1, Cyp4e3, Cyp4p1, Cyp4p2, Cyp6a14, Cyp6a17, Cyp6a2, Cyp6a20, Cyp6a21, Cyp6a22, Cyp6a23, Cyp6a9, Cyp6d2, Cyp6d4, Cyp9b1, Cyp9b2, Cyp9c1, Cyt-b5, Ero1L, Ire1, Kr-h2, P58IPK, PEK, SREBP, Sec22, Vti1b, Xport, gt, meigo, p115, scf
R-DME:381119	Unfolded Protein Response (UPR)	REACTOME	0.0250343	0	50.00	4	Ire1, PEK, eIF-2alpha, eIF-2beta
GO:0045182	translation regulator activity	GO_BP	0.0257336	0	11.82	13	CG2017, Dgp-1, P32, PEK, Thor, brat, eIF-2alpha, eIF-2beta, eIF2B-alpha, eIF2B-delta, eIF2B-epsilon, eIF2B-gamma, eIF2D
GO:0008033	tRNA processing	GO_BP	0.0277313	0	12.50	12	Aats-ala, CG10189, CG12264, CG18596, CG33785, CG33786, CG4611, CG6353, CG9987, Elp1, Elp2, JhI-1
GO:0031984	organelle subcompartment	GO_CC	0.0307778	0	6.37	39	Bet1, CG11796, CG13887, CG1942, CG42508, CG7083, CG7272, CG8311, CG9773, Cyp28a5, Cyp309a1, Cyp4ad1, Cyp4e3, Cyp4p1, Cyp4p2, Cyp6a14, Cyp6a17, Cyp6a2, Cyp6a20, Cyp6a21, Cyp6a22, Cyp6a23, Cyp6a9, Cyp6d2, Cyp6d4, Cyp9b1, Cyp9b2, Cyp9c1, Cyt-b5, Ero1L, Ire1, Nsf2, PEK, SREBP, Sec22, Vti1b, meigo, p115, rho
GO:0034982	mitochondrial protein processing	GO_BP	0.0432995	0	44.44	4	CG2658, CG6512, CG7791, CG8728
GO:0015803	branched-chain amino acid transport	GO_BP	0.0456372	0	75.00	3	CD98hc, CG5805, JhI-21
R-DME:381042	PERK regulates gene expression	REACTOME	0.0456372	0	75.00	3	PEK, eIF-2alpha, eIF-2beta

This figure is related to Figure 3a

I removed overlapping or similar terms for figure simplicity.

ClueGOResultTable_TUP_1.6_curr <- read.csv("Analysis/ClueGOResultTable_TUP_full_1.6_curated.csv",  header = TRUE, sep = ",")

ClueGOResultTable_TUP_1.6_curr  <- as.data.frame(ClueGOResultTable_TUP_1.6_curr )
ClueGOResultTable_TUP_1.6_curr  <- ClueGOResultTable_TUP_1.6_curr  %>% arrange((Term_PValue_Corrected_with_Bonferroni_step_down)) # arrage the data how you want it in the plot 
ClueGOResultTable_TUP_1.6_curr  <- ClueGOResultTable_TUP_1.6_curr  %>% mutate(GOTerm = fct_reorder(GOTerm, desc(Term_PValue_Corrected_with_Bonferroni_step_down))) # lock in factor level order

ClueGOResultTable_TUP_1.6_curr_plot <- ggplot( ClueGOResultTable_TUP_1.6_curr , aes(x = -log10(Term_PValue_Corrected_with_Bonferroni_step_down), y = GOTerm, fill= OS_short)) + geom_bar(stat="identity", width=0.7 ) + scale_fill_brewer(palette="RdBu") +  theme_bw() + ylab(NULL) + xlab("-log10(term adjusted p value)") + theme(legend.position="right", text = element_text(size=15)) + geom_text(aes(label=Nr_Genes ), size=3, nudge_x = .7, color = "black" ) + scale_x_continuous(expand = c(0, 0), limits = c(0, 12)) + guides(fill=guide_legend(title="Ontology")) 

ClueGOResultTable_TUP_1.6_curr_plot

ggsave("1.6_figure_output/ClueGOResultTable_TUP_1.6_curr_plot.pdf", scale = 1, dpi = 320, width = 11, height = 6, limitsize = TRUE)

ClueGo results: Downregulated transcripts

This table is related to Supplementary Table 10.

ClueGOResultTable_TDOWN_1.6 <- read.csv("Analysis/ClueGOResultTable_TDOWN_full_FC1.6.csv",  header = TRUE, sep = ",")
ClueGOResultTable_TDOWN_1.6 = ClueGOResultTable_TDOWN_1.6 %>% arrange(Term_PValue_Corrected_with_Bonferroni_step_down)

Table 12: ClueGO Results Table: Downregulated transcripts

GO ID	GO Term	Ontology	Term P-value corrected	Group P-value corrected	% Associated Genes	No. Genes	Associated Genes
GO:0016798	hydrolase activity, acting on glycosyl bonds	GO_MF	0.0000000	0.0000000	30.09	34	AGBE, Amyrel, CG13397, CG14823, CG15533, CG16756, CG16799, CG16965, CG31148, CG31414, CG33056, CG33080, CG6426, CG7997, CG9485, CG9701, GNBP3, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, LysP, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, alpha-Man-Ic, tobi
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	GO_MF	0.0000000	0.0000000	34.41	32	AGBE, Amyrel, CG13397, CG14823, CG16756, CG16799, CG16965, CG31148, CG31414, CG33080, CG6426, CG7997, CG9485, CG9701, GNBP3, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, LysP, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, alpha-Man-Ic, tobi
GO:0016798	hydrolase activity, acting on glycosyl bonds	GO_MF	0.0000000	0.0000000	30.09	34	AGBE, Amyrel, CG13397, CG14823, CG15533, CG16756, CG16799, CG16965, CG31148, CG31414, CG33056, CG33080, CG6426, CG7997, CG9485, CG9701, GNBP3, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, LysP, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, alpha-Man-Ic, tobi
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	GO_MF	0.0000000	0.0000000	34.41	32	AGBE, Amyrel, CG13397, CG14823, CG16756, CG16799, CG16965, CG31148, CG31414, CG33080, CG6426, CG7997, CG9485, CG9701, GNBP3, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, LysP, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, alpha-Man-Ic, tobi
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	GO_MF	0.0000000	0.0000000	34.41	32	AGBE, Amyrel, CG13397, CG14823, CG16756, CG16799, CG16965, CG31148, CG31414, CG33080, CG6426, CG7997, CG9485, CG9701, GNBP3, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, LysP, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, alpha-Man-Ic, tobi
GO:0016798	hydrolase activity, acting on glycosyl bonds	GO_MF	0.0000000	0.0000000	30.09	34	AGBE, Amyrel, CG13397, CG14823, CG15533, CG16756, CG16799, CG16965, CG31148, CG31414, CG33056, CG33080, CG6426, CG7997, CG9485, CG9701, GNBP3, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, LysP, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, alpha-Man-Ic, tobi
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	GO_MF	0.0000000	0.0000000	34.41	32	AGBE, Amyrel, CG13397, CG14823, CG16756, CG16799, CG16965, CG31148, CG31414, CG33080, CG6426, CG7997, CG9485, CG9701, GNBP3, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, LysP, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, alpha-Man-Ic, tobi
R-DME:1430728	Metabolism	REACTOME	0.0000000	0.0000000	9.62	117	Acox57D-d, AdenoK, Amnionless, CAH1, CDase, CG10026, CG11200, CG11236, CG11241, CG11438, CG12926, CG13369, CG13397, CG13898, CG14946, CG15093, CG1544, CG15553, CG16727, CG16756, CG16799, CG16935, CG16985, CG17224, CG18003, CG18258, CG18814, CG2187, CG31103, CG31414, CG33966, CG3534, CG3902, CG3940, CG42269, CG42514, CG4267, CG4752, CG4757, CG5162, CG5321, CG5958, CG5966, CG6126, CG6277, CG6283, CG6295, CG6465, CG6805, CG6910, CG7322, CG7882, CG7997, CG8028, CG8036, CG8534, CG8665, CG9509, CG9510, CG9629, CG9701, CG9886, CG9914, CRAT, CRMP, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Est-6, Fdh, Gal, Gale, Galt, Gk, Gnmt, GstT3, Hex-C, LKRSDH, LManI, LManIII, LManIV, LManV, LManVI, LysP, Men-b, Mtpalpha, Oat, Oatp58Da, Ppt2, Sardh, Spat, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, St1, UK114, arg, bgm, bmm, dare, dob, eas, fa2h, fabp, fbp, mdy, phm, pug, r-l, sea, su(r), sxe2
GO:0005615	extracellular space	GO_CC	0.0000000	0.0000000	9.88	73	Adgf-A, Ag5r, CG14132, CG14661, CG14990, CG15065, CG15199, CG15202, CG15533, CG16756, CG16799, CG17242, CG17974, CG18258, CG18284, CG18557, CG18563, CG2444, CG31148, CG31414, CG31704, CG31832, CG34033, CG34457, CG3534, CG3604, CG42326, CG4267, CG4408, CG4757, CG4847, CG5162, CG5402, CG5945, CG5966, CG6277, CG6283, CG6295, CG6426, CG7509, CG8093, CG9572, Cpr51A, Drs, Dup99B, Est-6, Fst, Gbp, IM33, Lsp1alpha, Lsp1beta, Lsp2, LysP, NLaz, Obp51a, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, TotA, TotM, TotX, Tsf1, l(3)72Dp, scw, ssp7, sxe2, tsl
GO:0005975	carbohydrate metabolic process	GO_BP	0.0000000	0.0000000	14.48	42	AGBE, Adgf-A, Amyrel, CG10467, CG11594, CG13369, CG1544, CG16965, CG32444, CG33080, CG3534, CG6805, CG6910, CG7322, CG7997, CG9485, CG9701, GNBP3, Gal, Gale, Galt, Gk, Gnmt, Hex-C, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, Sodh-1, alpha-Man-Ic, fbp, smp-30, tobi
GO:0005975	carbohydrate metabolic process	GO_BP	0.0000000	0.0000000	14.48	42	AGBE, Adgf-A, Amyrel, CG10467, CG11594, CG13369, CG1544, CG16965, CG32444, CG33080, CG3534, CG6805, CG6910, CG7322, CG7997, CG9485, CG9701, GNBP3, Gal, Gale, Galt, Gk, Gnmt, Hex-C, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, Sodh-1, alpha-Man-Ic, fbp, smp-30, tobi
GO:0005975	carbohydrate metabolic process	GO_BP	0.0000000	0.0000000	14.48	42	AGBE, Adgf-A, Amyrel, CG10467, CG11594, CG13369, CG1544, CG16965, CG32444, CG33080, CG3534, CG6805, CG6910, CG7322, CG7997, CG9485, CG9701, GNBP3, Gal, Gale, Galt, Gk, Gnmt, Hex-C, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, Sodh-1, alpha-Man-Ic, fbp, smp-30, tobi
GO:0005975	carbohydrate metabolic process	GO_BP	0.0000000	0.0000000	14.48	42	AGBE, Adgf-A, Amyrel, CG10467, CG11594, CG13369, CG1544, CG16965, CG32444, CG33080, CG3534, CG6805, CG6910, CG7322, CG7997, CG9485, CG9701, GNBP3, Gal, Gale, Galt, Gk, Gnmt, Hex-C, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, Sodh-1, alpha-Man-Ic, fbp, smp-30, tobi
KEGG:00052	Galactose metabolism	KEGG	0.0000000	0.0000000	41.67	15	CG10467, CG32444, CG7997, CG9436, Gal, Gale, Galt, Hex-C, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
KEGG:00052	Galactose metabolism	KEGG	0.0000000	0.0000000	41.67	15	CG10467, CG32444, CG7997, CG9436, Gal, Gale, Galt, Hex-C, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
KEGG:00052	Galactose metabolism	KEGG	0.0000000	0.0000000	41.67	15	CG10467, CG32444, CG7997, CG9436, Gal, Gale, Galt, Hex-C, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
R-DME:556833	Metabolism of lipids	REACTOME	0.0000000	0.0000000	12.00	48	Acox57D-d, CDase, CG11438, CG14946, CG16935, CG16985, CG18003, CG18258, CG18814, CG31414, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, CG6805, CG7997, CG8534, CG9701, CRAT, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Est-6, Gal, Gk, Mtpalpha, Ppt2, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, bgm, bmm, dob, eas, fa2h, fabp, mdy, phm, sea, sxe2
R-DME:556833	Metabolism of lipids	REACTOME	0.0000000	0.0000000	12.00	48	Acox57D-d, CDase, CG11438, CG14946, CG16935, CG16985, CG18003, CG18258, CG18814, CG31414, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, CG6805, CG7997, CG8534, CG9701, CRAT, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Est-6, Gal, Gk, Mtpalpha, Ppt2, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, bgm, bmm, dob, eas, fa2h, fabp, mdy, phm, sea, sxe2
R-DME:556833	Metabolism of lipids	REACTOME	0.0000000	0.0000000	12.00	48	Acox57D-d, CDase, CG11438, CG14946, CG16935, CG16985, CG18003, CG18258, CG18814, CG31414, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, CG6805, CG7997, CG8534, CG9701, CRAT, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Est-6, Gal, Gk, Mtpalpha, Ppt2, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, bgm, bmm, dob, eas, fa2h, fabp, mdy, phm, sea, sxe2
R-DME:556833	Metabolism of lipids	REACTOME	0.0000000	0.0000000	12.00	48	Acox57D-d, CDase, CG11438, CG14946, CG16935, CG16985, CG18003, CG18258, CG18814, CG31414, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, CG6805, CG7997, CG8534, CG9701, CRAT, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Est-6, Gal, Gk, Mtpalpha, Ppt2, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, bgm, bmm, dob, eas, fa2h, fabp, mdy, phm, sea, sxe2
GO:0015926	glucosidase activity	GO_MF	0.0000000	0.0000000	62.50	10	CG16965, CG9485, CG9701, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
GO:0015926	glucosidase activity	GO_MF	0.0000000	0.0000000	62.50	10	CG16965, CG9485, CG9701, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
GO:0044282	small molecule catabolic process	GO_BP	0.0000001	0.0000000	15.47	28	Acox57D-d, Adgf-A, CG10361, CG10467, CG11236, CG13369, CG15093, CG32444, CG3699, CG6805, CG6910, CG8129, CG8665, CRAT, Cp38, Dat, Fdh, Gale, Galt, Gk, LKRSDH, Mtpalpha, Oat, Sardh, Sodh-1, Spat, arg, dare
GO:0090599	alpha-glucosidase activity	GO_MF	0.0000007	0.0000000	66.67	8	CG9485, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
GO:0006082	organic acid metabolic process	GO_BP	0.0000020	0.0000000	10.07	43	Acox57D-d, CDase, CG10361, CG11236, CG11407, CG15093, CG1544, CG16935, CG31076, CG3603, CG3699, CG4830, CG5568, CG6465, CG6733, CG8129, CG8534, CG8665, CG8834, CG9510, CG9914, CG9993, CRAT, Cp38, FASN3, Gip, Gnmt, Hex-C, Irp-1B, LKRSDH, Men-b, Mtpalpha, Oat, Sardh, Spat, arg, bgm, fa2h, mdy, phm, pug, smp-30, su(r)
GO:0006082	organic acid metabolic process	GO_BP	0.0000020	0.0000000	10.07	43	Acox57D-d, CDase, CG10361, CG11236, CG11407, CG15093, CG1544, CG16935, CG31076, CG3603, CG3699, CG4830, CG5568, CG6465, CG6733, CG8129, CG8534, CG8665, CG8834, CG9510, CG9914, CG9993, CRAT, Cp38, FASN3, Gip, Gnmt, Hex-C, Irp-1B, LKRSDH, Men-b, Mtpalpha, Oat, Sardh, Spat, arg, bgm, fa2h, mdy, phm, pug, smp-30, su(r)
GO:0019752	carboxylic acid metabolic process	GO_BP	0.0000021	0.0000000	10.19	42	Acox57D-d, CDase, CG10361, CG11236, CG11407, CG15093, CG1544, CG16935, CG31076, CG3603, CG3699, CG4830, CG5568, CG6465, CG6733, CG8129, CG8534, CG8665, CG8834, CG9510, CG9914, CG9993, CRAT, Cp38, FASN3, Gip, Gnmt, Hex-C, Irp-1B, LKRSDH, Men-b, Mtpalpha, Oat, Sardh, Spat, arg, bgm, fa2h, mdy, pug, smp-30, su(r)
GO:0019752	carboxylic acid metabolic process	GO_BP	0.0000021	0.0000000	10.19	42	Acox57D-d, CDase, CG10361, CG11236, CG11407, CG15093, CG1544, CG16935, CG31076, CG3603, CG3699, CG4830, CG5568, CG6465, CG6733, CG8129, CG8534, CG8665, CG8834, CG9510, CG9914, CG9993, CRAT, Cp38, FASN3, Gip, Gnmt, Hex-C, Irp-1B, LKRSDH, Men-b, Mtpalpha, Oat, Sardh, Spat, arg, bgm, fa2h, mdy, pug, smp-30, su(r)
GO:0043436	oxoacid metabolic process	GO_BP	0.0000026	0.0000000	10.12	42	Acox57D-d, CDase, CG10361, CG11236, CG11407, CG15093, CG1544, CG16935, CG31076, CG3603, CG3699, CG4830, CG5568, CG6465, CG6733, CG8129, CG8534, CG8665, CG8834, CG9510, CG9914, CG9993, CRAT, Cp38, FASN3, Gip, Gnmt, Hex-C, Irp-1B, LKRSDH, Men-b, Mtpalpha, Oat, Sardh, Spat, arg, bgm, fa2h, mdy, pug, smp-30, su(r)
GO:0043436	oxoacid metabolic process	GO_BP	0.0000026	0.0000000	10.12	42	Acox57D-d, CDase, CG10361, CG11236, CG11407, CG15093, CG1544, CG16935, CG31076, CG3603, CG3699, CG4830, CG5568, CG6465, CG6733, CG8129, CG8534, CG8665, CG8834, CG9510, CG9914, CG9993, CRAT, Cp38, FASN3, Gip, Gnmt, Hex-C, Irp-1B, LKRSDH, Men-b, Mtpalpha, Oat, Sardh, Spat, arg, bgm, fa2h, mdy, pug, smp-30, su(r)
GO:0005996	monosaccharide metabolic process	GO_BP	0.0000030	0.0000000	20.99	17	CG10467, CG13369, CG32444, CG3534, CG7322, Gal, Gale, Galt, Gnmt, Hex-C, LManI, LManIII, LManIV, LManV, LManVI, fbp, smp-30
GO:0005996	monosaccharide metabolic process	GO_BP	0.0000030	0.0000000	20.99	17	CG10467, CG13369, CG32444, CG3534, CG7322, Gal, Gale, Galt, Gnmt, Hex-C, LManI, LManIII, LManIV, LManV, LManVI, fbp, smp-30
GO:0005996	monosaccharide metabolic process	GO_BP	0.0000030	0.0000000	20.99	17	CG10467, CG13369, CG32444, CG3534, CG7322, Gal, Gale, Galt, Gnmt, Hex-C, LManI, LManIII, LManIV, LManV, LManVI, fbp, smp-30
GO:0000023	maltose metabolic process	GO_BP	0.0000049	0.0000000	70.00	7	Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
GO:0032450	maltose alpha-glucosidase activity	GO_BP	0.0000049	0.0000000	70.00	7	Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
GO:0004558	alpha-1,4-glucosidase activity	GO_MF	0.0000049	0.0000000	70.00	7	Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
R-DME:71387	Metabolism of carbohydrates	REACTOME	0.0000050	0.0000000	15.23	23	CG13369, CG13397, CG13898, CG16756, CG16799, CG3534, CG7322, CG7882, CG8036, CG9886, CG9914, Gal, Gale, Galt, Hex-C, LManI, LManIII, LManIV, LManV, LManVI, LysP, fbp, sea
R-DME:8963743	Digestion and absorption	REACTOME	0.0000054	0.0000000	20.24	17	Amyrel, CG18258, CG18284, CG18302, CG31091, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG7882, CG8093, CG9701, Lip4, Npc1b, sxe2
KEGG:00500	Starch and sucrose metabolism	KEGG	0.0000055	0.0000000	34.38	11	AGBE, Amyrel, CG9485, Hex-C, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
KEGG:00500	Starch and sucrose metabolism	KEGG	0.0000055	0.0000000	34.38	11	AGBE, Amyrel, CG9485, Hex-C, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1
GO:0004867	serine-type endopeptidase inhibitor activity	GO_BP	0.0000065	0.0000000	20.00	17	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0004867	serine-type endopeptidase inhibitor activity	GO_BP	0.0000065	0.0000235	20.00	17	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0016042	lipid catabolic process	GO_BP	0.0000068	0.0000000	14.46	24	Acox57D-d, CDase, CG15533, CG18258, CG18302, CG31091, CG31148, CG31414, CG3699, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG7997, CG8093, CRAT, Lip4, Mtpalpha, bmm, dare, dob, sxe2
GO:0016042	lipid catabolic process	GO_BP	0.0000068	0.0000000	14.46	24	Acox57D-d, CDase, CG15533, CG18258, CG18302, CG31091, CG31148, CG31414, CG3699, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG7997, CG8093, CRAT, Lip4, Mtpalpha, bmm, dare, dob, sxe2
GO:0016042	lipid catabolic process	GO_BP	0.0000068	0.0000000	14.46	24	Acox57D-d, CDase, CG15533, CG18258, CG18302, CG31091, CG31148, CG31414, CG3699, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG7997, CG8093, CRAT, Lip4, Mtpalpha, bmm, dare, dob, sxe2
GO:0004806	triglyceride lipase activity	GO_MF	0.0000073	0.0000000	22.73	15	CG18258, CG18284, CG18302, CG31091, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG8093, Lip4, bmm, dob, sxe2
GO:0004806	triglyceride lipase activity	GO_MF	0.0000073	0.0000000	22.73	15	CG18258, CG18284, CG18302, CG31091, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG8093, Lip4, bmm, dob, sxe2
GO:0017171	serine hydrolase activity	GO_BP	0.0000132	0.0000235	10.31	37	CG10031, CG11034, CG14298, CG14990, CG16704, CG17242, CG1773, CG18179, CG18557, CG18563, CG30090, CG30371, CG31777, CG31821, CG34457, CG3604, CG3734, CG3739, CG42465, CG42828, CG8299, CG9649, IM33, Jon25Bii, Jon99Ci, Phae1, Phae2, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, Tequila
GO:0008236	serine-type peptidase activity	GO_BP	0.0000132	0.0000235	10.31	37	CG10031, CG11034, CG14298, CG14990, CG16704, CG17242, CG1773, CG18179, CG18557, CG18563, CG30090, CG30371, CG31777, CG31821, CG34457, CG3604, CG3734, CG3739, CG42465, CG42828, CG8299, CG9649, IM33, Jon25Bii, Jon99Ci, Phae1, Phae2, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, Tequila
GO:0004866	endopeptidase inhibitor activity	GO_BP	0.0000190	0.0000235	17.65	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0061135	endopeptidase regulator activity	GO_BP	0.0000258	0.0000235	17.31	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0030414	peptidase inhibitor activity	GO_BP	0.0000300	0.0000235	17.14	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0010951	negative regulation of endopeptidase activity	GO_BP	0.0000300	0.0000235	17.14	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
KEGG:00511	Other glycan degradation	KEGG	0.0000313	0.0000000	39.13	9	CG31148, CG31414, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI
KEGG:00511	Other glycan degradation	KEGG	0.0000313	0.0000000	39.13	9	CG31148, CG31414, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI
GO:0052689	carboxylic ester hydrolase activity	GO_MF	0.0000330	0.0000000	14.29	22	CG18258, CG18284, CG18302, CG31091, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, CG8093, Est-6, Lip4, alpha-Est10, alpha-Est2, alpha-Est5, alpha-Est7, bmm, dob, smp-30, sxe2
GO:0010466	negative regulation of peptidase activity	GO_BP	0.0000466	0.0000235	16.67	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:192456	Digestion of dietary lipid	REACTOME	0.0000494	0.0000000	23.21	13	CG18258, CG18284, CG18302, CG31091, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG8093, Lip4, sxe2
GO:0006629	lipid metabolic process	GO_BP	0.0000529	0.0000000	8.25	51	Acox57D-d, CDase, CG11200, CG11407, CG11438, CG15533, CG16935, CG17560, CG17562, CG18031, CG18258, CG18284, CG18302, CG31091, CG31148, CG31414, CG3603, CG3699, CG4020, CG4267, CG4830, CG5162, CG5568, CG5966, CG6277, CG6283, CG6295, CG6805, CG7997, CG8093, CG8534, CG8834, CG9509, CG9914, CG9993, CRAT, FASN3, Gk, Lip4, Mtpalpha, NLaz, Npc1b, bgm, bmm, dare, dob, eas, fa2h, mdy, phm, sxe2
GO:0006629	lipid metabolic process	GO_BP	0.0000529	0.0000000	8.25	51	Acox57D-d, CDase, CG11200, CG11407, CG11438, CG15533, CG16935, CG17560, CG17562, CG18031, CG18258, CG18284, CG18302, CG31091, CG31148, CG31414, CG3603, CG3699, CG4020, CG4267, CG4830, CG5162, CG5568, CG5966, CG6277, CG6283, CG6295, CG6805, CG7997, CG8093, CG8534, CG8834, CG9509, CG9914, CG9993, CRAT, FASN3, Gk, Lip4, Mtpalpha, NLaz, Npc1b, bgm, bmm, dare, dob, eas, fa2h, mdy, phm, sxe2
GO:0006629	lipid metabolic process	GO_BP	0.0000529	0.0000000	8.25	51	Acox57D-d, CDase, CG11200, CG11407, CG11438, CG15533, CG16935, CG17560, CG17562, CG18031, CG18258, CG18284, CG18302, CG31091, CG31148, CG31414, CG3603, CG3699, CG4020, CG4267, CG4830, CG5162, CG5568, CG5966, CG6277, CG6283, CG6295, CG6805, CG7997, CG8093, CG8534, CG8834, CG9509, CG9914, CG9993, CRAT, FASN3, Gk, Lip4, Mtpalpha, NLaz, Npc1b, bgm, bmm, dare, dob, eas, fa2h, mdy, phm, sxe2
GO:0006629	lipid metabolic process	GO_BP	0.0000529	0.0000000	8.25	51	Acox57D-d, CDase, CG11200, CG11407, CG11438, CG15533, CG16935, CG17560, CG17562, CG18031, CG18258, CG18284, CG18302, CG31091, CG31148, CG31414, CG3603, CG3699, CG4020, CG4267, CG4830, CG5162, CG5568, CG5966, CG6277, CG6283, CG6295, CG6805, CG7997, CG8093, CG8534, CG8834, CG9509, CG9914, CG9993, CRAT, FASN3, Gk, Lip4, Mtpalpha, NLaz, Npc1b, bgm, bmm, dare, dob, eas, fa2h, mdy, phm, sxe2
R-DME:8935690	Digestion	REACTOME	0.0000639	0.0000000	19.48	15	Amyrel, CG18258, CG18284, CG18302, CG31091, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG8093, CG9701, Lip4, sxe2
GO:0061134	peptidase regulator activity	GO_BP	0.0000817	0.0000235	16.07	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0044262	cellular carbohydrate metabolic process	GO_BP	0.0000927	0.0000000	15.20	19	AGBE, CG11594, CG13369, CG3534, CG6805, CG6910, CG9485, Gk, Gnmt, Hex-C, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, Sodh-1, fbp
GO:0044262	cellular carbohydrate metabolic process	GO_BP	0.0000927	0.0000000	15.20	19	AGBE, CG11594, CG13369, CG3534, CG6805, CG6910, CG9485, Gk, Gnmt, Hex-C, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, Sodh-1, fbp
KEGG:00040	Pentose and glucuronate interconversions	KEGG	0.0001012	0.0000026	24.00	12	CG15661, CG17322, CG17324, CG3534, CG3597, CG3609, CG4302, CG7322, CG9436, CG9914, Sodh-1, Ugt37b1
GO:0019318	hexose metabolic process	GO_BP	0.0001400	0.0000000	19.72	14	CG10467, CG32444, CG7322, Gal, Gale, Galt, Gnmt, Hex-C, LManI, LManIII, LManIV, LManV, LManVI, fbp
GO:0019318	hexose metabolic process	GO_BP	0.0001400	0.0000000	19.72	14	CG10467, CG32444, CG7322, Gal, Gale, Galt, Gnmt, Hex-C, LManI, LManIII, LManIV, LManV, LManVI, fbp
GO:0019318	hexose metabolic process	GO_BP	0.0001400	0.0000000	19.72	14	CG10467, CG32444, CG7322, Gal, Gale, Galt, Gnmt, Hex-C, LManI, LManIII, LManIV, LManV, LManVI, fbp
GO:0005984	disaccharide metabolic process	GO_BP	0.0002111	0.0000000	38.10	8	Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, fbp
KEGG:00260	Glycine, serine and threonine metabolism	KEGG	0.0002168	0.0000050	32.14	9	CG10361, CG11236, CG11241, CG8129, CG9629, CG9886, Gnmt, Sardh, Spat
GO:0046394	carboxylic acid biosynthetic process	GO_BP	0.0002220	0.0000000	13.79	20	CDase, CG11407, CG16935, CG3603, CG4830, CG5568, CG8534, CG8834, CG9510, CG9993, FASN3, Gnmt, LKRSDH, Oat, Spat, bgm, fa2h, pug, smp-30, su(r)
GO:0004252	serine-type endopeptidase activity	GO_BP	0.0002339	0.0000235	9.79	33	CG10031, CG14298, CG14990, CG16704, CG17242, CG1773, CG18179, CG18557, CG18563, CG30090, CG30371, CG31777, CG34457, CG3604, CG42465, CG42828, CG8299, CG9649, IM33, Jon25Bii, Jon99Ci, Phae1, Phae2, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, Tequila
KEGG:04142	Lysosome	KEGG	0.0002624	0.0000000	14.88	18	CG13397, CG13516, CG31148, CG31414, CG4847, CG7997, DNaseII, Gal, Hexo1, LManI, LManIII, LManIV, LManV, LManVI, Lip4, Npc1b, Ppt2, Vha100-5
GO:0045861	negative regulation of proteolysis	GO_BP	0.0002964	0.0000235	14.75	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0016053	organic acid biosynthetic process	GO_BP	0.0003807	0.0000000	13.33	20	CDase, CG11407, CG16935, CG3603, CG4830, CG5568, CG8534, CG8834, CG9510, CG9993, FASN3, Gnmt, LKRSDH, Oat, Spat, bgm, fa2h, pug, smp-30, su(r)
GO:1901575	organic substance catabolic process	GO_BP	0.0005840	0.0000000	6.84	67	Acox57D-d, Adgf-A, CDase, CG10361, CG10467, CG11236, CG12917, CG13369, CG15093, CG1544, CG15533, CG17224, CG18258, CG18302, CG31091, CG31148, CG31414, CG32444, CG33346, CG3699, CG3819, CG4267, CG4847, CG5162, CG5966, CG6277, CG6283, CG6295, CG6805, CG6910, CG7997, CG8093, CG8129, CG8665, CG9485, CRAT, CRMP, Cp38, DNaseII, Dat, Dcp-1, Est-6, Fdh, Gale, Galt, Gk, Gnmt, Hex-C, Kdm2, LKRSDH, Lip4, Mtpalpha, Oat, PGRP-SB1, PGRP-SC1a, PGRP-SC2, Sardh, Sid, Sodh-1, Spat, UK114, arg, bmm, dare, dob, su(r), sxe2
GO:1901575	organic substance catabolic process	GO_BP	0.0005840	0.0000000	6.84	67	Acox57D-d, Adgf-A, CDase, CG10361, CG10467, CG11236, CG12917, CG13369, CG15093, CG1544, CG15533, CG17224, CG18258, CG18302, CG31091, CG31148, CG31414, CG32444, CG33346, CG3699, CG3819, CG4267, CG4847, CG5162, CG5966, CG6277, CG6283, CG6295, CG6805, CG6910, CG7997, CG8093, CG8129, CG8665, CG9485, CRAT, CRMP, Cp38, DNaseII, Dat, Dcp-1, Est-6, Fdh, Gale, Galt, Gk, Gnmt, Hex-C, Kdm2, LKRSDH, Lip4, Mtpalpha, Oat, PGRP-SB1, PGRP-SC1a, PGRP-SC2, Sardh, Sid, Sodh-1, Spat, UK114, arg, bmm, dare, dob, su(r), sxe2
R-DME:8853383	Lysosomal oligosaccharide catabolism	REACTOME	0.0005867	0.0000000	71.43	5	LManI, LManIII, LManIV, LManV, LManVI
GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	GO_MF	0.0006674	0.0000139	13.38	19	CG11200, CG12116, CG14946, CG15093, CG18003, CG18814, CG3301, CG3603, CG3699, CG7322, CG9436, CG9509, CG9914, FASN3, Fdh, Hex-C, Men-b, Mtpalpha, Sodh-1
GO:0016298	lipase activity	GO_MF	0.0007767	0.0000000	15.24	16	CG15533, CG18258, CG18284, CG18302, CG31091, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG8093, Lip4, bmm, dob, sxe2
GO:0016298	lipase activity	GO_MF	0.0007767	0.0000000	15.24	16	CG15533, CG18258, CG18284, CG18302, CG31091, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, CG8093, Lip4, bmm, dob, sxe2
GO:0032787	monocarboxylic acid metabolic process	GO_BP	0.0008206	0.0000000	11.50	23	Acox57D-d, CDase, CG11407, CG1544, CG16935, CG31076, CG3603, CG3699, CG4830, CG5568, CG8534, CG8834, CG9914, CG9993, CRAT, FASN3, Gip, Hex-C, Men-b, Mtpalpha, Spat, bgm, fa2h
GO:0009410	response to xenobiotic stimulus	GO_BP	0.0009185	0.0000169	38.89	7	CG17322, CG17324, Cyp6t1, Cyp6w1, St1, St3, phm
GO:0006805	xenobiotic metabolic process	GO_BP	0.0009185	0.0000169	38.89	7	CG17322, CG17324, Cyp6t1, Cyp6w1, St1, St3, phm
GO:0071466	cellular response to xenobiotic stimulus	GO_BP	0.0009185	0.0000169	38.89	7	CG17322, CG17324, Cyp6t1, Cyp6w1, St1, St3, phm
GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	GO_MF	0.0009292	0.0000139	14.29	17	CG11200, CG12116, CG14946, CG15093, CG18814, CG3301, CG3603, CG3699, CG7322, CG9436, CG9914, FASN3, Fdh, Hex-C, Men-b, Mtpalpha, Sodh-1
R-DME:196071	Metabolism of steroid hormones	REACTOME	0.0013614	0.0000000	19.05	12	CG14946, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:196071	Metabolism of steroid hormones	REACTOME	0.0013614	0.0000235	19.05	12	CG14946, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0004175	endopeptidase activity	GO_BP	0.0017231	0.0000235	7.88	43	AdamTS-A, CG10031, CG14298, CG14526, CG14528, CG14990, CG16704, CG17242, CG1773, CG18179, CG18557, CG18563, CG30090, CG30371, CG31777, CG34457, CG3604, CG3775, CG42465, CG42828, CG4721, CG4847, CG5715, CG8066, CG8299, CG8550, CG9649, Dcp-1, IM33, Jon25Bii, Jon99Ci, Phae1, Phae2, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, Tequila
GO:0004857	enzyme inhibitor activity	GO_BP	0.0019638	0.0000235	12.95	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0051346	negative regulation of hydrolase activity	GO_BP	0.0024017	0.0000235	12.77	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0052548	regulation of endopeptidase activity	GO_BP	0.0024017	0.0000235	12.77	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0004559	alpha-mannosidase activity	GO_MF	0.0025232	0.0000000	42.86	6	LManI, LManIII, LManIV, LManV, LManVI, alpha-Man-Ic
GO:0035337	fatty-acyl-CoA metabolic process	GO_BP	0.0027452	0.0000016	24.32	9	CG11407, CG17560, CG17562, CG18031, CG4020, CG4830, CG5568, CG8834, CG9993
GO:0035337	fatty-acyl-CoA metabolic process	GO_BP	0.0027452	0.0000000	24.32	9	CG11407, CG17560, CG17562, CG18031, CG4020, CG4830, CG5568, CG8834, CG9993
R-DME:8957322	Metabolism of steroids	REACTOME	0.0027944	0.0000000	14.56	15	Acox57D-d, CG14946, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, fabp, phm
R-DME:8957322	Metabolism of steroids	REACTOME	0.0027944	0.0000000	14.56	15	Acox57D-d, CG14946, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, fabp, phm
R-DME:8957322	Metabolism of steroids	REACTOME	0.0027944	0.0000235	14.56	15	Acox57D-d, CG14946, Cyp4ac1, Cyp4ac2, Cyp4d8, Cyp4s3, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, fabp, phm
R-DME:1483206	Glycerophospholipid biosynthesis	REACTOME	0.0031450	0.0000000	14.42	15	CG18258, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, Est-6, Mtpalpha, bmm, dob, eas, mdy, sxe2
R-DME:1483206	Glycerophospholipid biosynthesis	REACTOME	0.0031450	0.0000000	14.42	15	CG18258, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, Est-6, Mtpalpha, bmm, dob, eas, mdy, sxe2
GO:0015923	mannosidase activity	GO_MF	0.0040271	0.0000000	40.00	6	LManI, LManIII, LManIV, LManV, LManVI, alpha-Man-Ic
GO:0052547	regulation of peptidase activity	GO_BP	0.0046761	0.0000235	12.16	18	CG10031, CG14298, CG16704, CG31777, CG3604, CG42465, CG42828, CG8066, IM33, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:1901568	fatty acid derivative metabolic process	GO_BP	0.0053783	0.0000016	22.50	9	CG11407, CG17560, CG17562, CG18031, CG4020, CG4830, CG5568, CG8834, CG9993
GO:0009311	oligosaccharide metabolic process	GO_BP	0.0053783	0.0000000	22.50	9	CG7997, Mal-A1, Mal-A2, Mal-A3, Mal-A4, Mal-A7, Mal-A8, Mal-B1, fbp
GO:1901568	fatty acid derivative metabolic process	GO_BP	0.0053783	0.0000000	22.50	9	CG11407, CG17560, CG17562, CG18031, CG4020, CG4830, CG5568, CG8834, CG9993
R-DME:8939242	RUNX1 regulates transcription of genes involved in differentiation of keratinocytes	REACTOME	0.0054760	0.0000000	25.81	8	CG4847, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:8939242	RUNX1 regulates transcription of genes involved in differentiation of keratinocytes	REACTOME	0.0054760	0.0000235	25.81	8	CG4847, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0006013	mannose metabolic process	GO_BP	0.0061010	0.0000000	50.00	5	LManI, LManIII, LManIV, LManV, LManVI
GO:0006631	fatty acid metabolic process	GO_BP	0.0061557	0.0000000	12.41	17	Acox57D-d, CDase, CG11407, CG16935, CG3603, CG3699, CG4830, CG5568, CG8534, CG8834, CG9914, CG9993, CRAT, FASN3, Mtpalpha, bgm, fa2h
GO:0006631	fatty acid metabolic process	GO_BP	0.0061557	0.0000000	12.41	17	Acox57D-d, CDase, CG11407, CG16935, CG3603, CG3699, CG4830, CG5568, CG8534, CG8834, CG9914, CG9993, CRAT, FASN3, Mtpalpha, bgm, fa2h
R-DME:425407	SLC-mediated transmembrane transport	REACTOME	0.0070223	0.0000965	10.09	23	CG10960, CG1208, CG1213, CG13795, CG15096, CG16727, CG2187, CG31103, CG42269, CG6126, CG6484, CG7255, CG7882, CG8028, CG8083, CG8249, CG9864, MFS14, Mal-A2, NaPi-T, Oatp58Da, ZnT77C, slif
GO:0046395	carboxylic acid catabolic process	GO_BP	0.0085313	0.0000000	13.27	15	Acox57D-d, CG10361, CG11236, CG15093, CG3699, CG8129, CG8665, CRAT, Cp38, LKRSDH, Mtpalpha, Oat, Sardh, Spat, arg
GO:0046395	carboxylic acid catabolic process	GO_BP	0.0085313	0.0000000	13.27	15	Acox57D-d, CG10361, CG11236, CG15093, CG3699, CG8129, CG8665, CRAT, Cp38, LKRSDH, Mtpalpha, Oat, Sardh, Spat, arg
GO:0044283	small molecule biosynthetic process	GO_BP	0.0089933	0.0000000	9.09	27	Adgf-A, CDase, CG11407, CG12116, CG16935, CG17224, CG3603, CG4830, CG5568, CG8534, CG8834, CG9510, CG9993, FASN3, Gnmt, LKRSDH, Npc1b, Oat, Spat, bgm, dare, fa2h, fbp, phm, pug, smp-30, su(r)
R-DME:8979227	Triglyceride metabolism	REACTOME	0.0106881	0.0001184	45.45	5	Gk, bmm, dob, fabp, mdy
GO:0006012	galactose metabolic process	GO_BP	0.0106881	0.0000000	45.45	5	CG10467, CG32444, Gal, Gale, Galt
GO:0006012	galactose metabolic process	GO_BP	0.0106881	0.0000000	45.45	5	CG10467, CG32444, Gal, Gale, Galt
GO:0006012	galactose metabolic process	GO_BP	0.0106881	0.0000000	45.45	5	CG10467, CG32444, Gal, Gale, Galt
R-DME:2022377	Metabolism of Angiotensinogen to Angiotensins	REACTOME	0.0107758	0.0000000	13.73	14	CG14526, CG14528, CG3775, CG4721, CG4757, CG8550, Est-6, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:2022377	Metabolism of Angiotensinogen to Angiotensins	REACTOME	0.0107758	0.0000235	13.73	14	CG14526, CG14528, CG3775, CG4721, CG4757, CG8550, Est-6, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:1482801	Acyl chain remodelling of PS	REACTOME	0.0111505	0.0000000	23.53	8	CG18258, CG4267, CG5162, CG5966, CG6277, CG6283, CG6295, sxe2
GO:0016054	organic acid catabolic process	GO_BP	0.0127703	0.0000000	12.82	15	Acox57D-d, CG10361, CG11236, CG15093, CG3699, CG8129, CG8665, CRAT, Cp38, LKRSDH, Mtpalpha, Oat, Sardh, Spat, arg
GO:0016054	organic acid catabolic process	GO_BP	0.0127703	0.0000000	12.82	15	Acox57D-d, CG10361, CG11236, CG15093, CG3699, CG8129, CG8665, CRAT, Cp38, LKRSDH, Mtpalpha, Oat, Sardh, Spat, arg
R-DME:196854	Metabolism of vitamins and cofactors	REACTOME	0.0142894	0.0001201	11.18	18	Amnionless, CG10026, CG11200, CG12926, CG13898, CG15553, CG16727, CG2187, CG31103, CG33966, CG42269, CG42514, CG5958, CG6126, CG7882, CG8665, fabp, pug
GO:0008233	peptidase activity	GO_BP	0.0150124	0.0000235	6.85	49	AdamTS-A, CG10031, CG11034, CG14298, CG14526, CG14528, CG14990, CG16704, CG17242, CG1773, CG18179, CG18557, CG18563, CG30090, CG30371, CG31777, CG31821, CG34457, CG3604, CG3734, CG3739, CG3775, CG42465, CG42828, CG4408, CG4721, CG4847, CG5715, CG8066, CG8299, CG8550, CG9649, Dcp-1, IM33, Jon25Bii, Jon99Ci, Phae1, Phae2, Sfp24Ba, Sfp24Bb, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, Tequila, l(3)72Dp
GO:0016788	hydrolase activity, acting on ester bonds	GO_MF	0.0166178	0.0000000	7.10	44	Alp2, CG11291, CG11438, CG12917, CG15533, CG16985, CG18258, CG18284, CG18302, CG18473, CG2145, CG31091, CG31812, CG32191, CG33082, CG33346, CG3819, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, CG6805, CG8093, CG9119, DNaseII, Est-6, FASN3, LanB1, Lip4, Ppt2, Sid, alpha-Est10, alpha-Est2, alpha-Est5, alpha-Est7, bmm, dob, fbp, mre11, smp-30, sxe2
R-DME:1474290	Collagen formation	REACTOME	0.0170197	0.0000000	19.57	9	CG4847, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, lox2
R-DME:1474290	Collagen formation	REACTOME	0.0170197	0.0000235	19.57	9	CG4847, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, lox2
GO:0006633	fatty acid biosynthetic process	GO_BP	0.0181162	0.0000016	14.81	12	CDase, CG11407, CG16935, CG3603, CG4830, CG5568, CG8534, CG8834, CG9993, FASN3, bgm, fa2h
GO:0006633	fatty acid biosynthetic process	GO_BP	0.0181162	0.0000000	14.81	12	CDase, CG11407, CG16935, CG3603, CG4830, CG5568, CG8534, CG8834, CG9993, FASN3, bgm, fa2h
R-DME:1483257	Phospholipid metabolism	REACTOME	0.0184855	0.0000000	11.85	16	CG18258, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, CG6805, Est-6, Mtpalpha, bmm, dob, eas, mdy, sxe2
R-DME:1483257	Phospholipid metabolism	REACTOME	0.0184855	0.0000000	11.85	16	CG18258, CG4267, CG4757, CG5162, CG5966, CG6277, CG6283, CG6295, CG6805, Est-6, Mtpalpha, bmm, dob, eas, mdy, sxe2
GO:0006066	alcohol metabolic process	GO_BP	0.0186299	0.0001062	12.40	15	CDase, CG11200, CG12116, CG18814, CG6805, CG6910, Dat, Fdh, Gbp, Gk, Npc1b, Sodh-1, dare, mdy, phm
R-DME:1482883	Acyl chain remodeling of DAG and TAG	REACTOME	0.0190705	0.0001184	100.00	3	bmm, dob, mdy
GO:0035383	thioester metabolic process	GO_BP	0.0234473	0.0000016	16.95	10	CG11407, CG17560, CG17562, CG18031, CG4020, CG4830, CG5568, CG8834, CG9993, LKRSDH
GO:0006637	acyl-CoA metabolic process	GO_BP	0.0234473	0.0000016	16.95	10	CG11407, CG17560, CG17562, CG18031, CG4020, CG4830, CG5568, CG8834, CG9993, LKRSDH
GO:0035383	thioester metabolic process	GO_BP	0.0234473	0.0000000	16.95	10	CG11407, CG17560, CG17562, CG18031, CG4020, CG4830, CG5568, CG8834, CG9993, LKRSDH
GO:0006637	acyl-CoA metabolic process	GO_BP	0.0234473	0.0000000	16.95	10	CG11407, CG17560, CG17562, CG18031, CG4020, CG4830, CG5568, CG8834, CG9993, LKRSDH
GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	GO_MF	0.0254699	0.0000016	21.05	8	CG17560, CG17562, CG18031, CG31076, CG4020, CG8665, CG9629, Fdh
GO:0072330	monocarboxylic acid biosynthetic process	GO_BP	0.0256621	0.0000016	14.29	12	CDase, CG11407, CG16935, CG3603, CG4830, CG5568, CG8534, CG8834, CG9993, FASN3, bgm, fa2h
GO:0072330	monocarboxylic acid biosynthetic process	GO_BP	0.0256621	0.0000000	14.29	12	CDase, CG11407, CG16935, CG3603, CG4830, CG5568, CG8534, CG8834, CG9993, FASN3, bgm, fa2h
R-DME:1474244	Extracellular matrix organization	REACTOME	0.0287875	0.0000000	14.12	12	AdamTS-A, CG4847, LanB1, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, lox2, scw
R-DME:1474244	Extracellular matrix organization	REACTOME	0.0287875	0.0000235	14.12	12	AdamTS-A, CG4847, LanB1, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb, lox2, scw
R-DME:2980736	Peptide hormone metabolism	REACTOME	0.0295000	0.0000000	12.50	14	CG14526, CG14528, CG3775, CG4721, CG4757, CG8550, Est-6, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:2980736	Peptide hormone metabolism	REACTOME	0.0295000	0.0000235	12.50	14	CG14526, CG14528, CG3775, CG4721, CG4757, CG8550, Est-6, Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0006790	sulfur compound metabolic process	GO_BP	0.0315648	0.0000016	10.16	19	CG11407, CG17560, CG17562, CG18031, CG4020, CG4752, CG4830, CG5568, CG8834, CG9993, Cp38, Gnmt, GstE13, GstT3, LKRSDH, Sardh, St1, St3, pug
GO:0016052	carbohydrate catabolic process	GO_BP	0.0348944	0.0000000	14.86	11	CG10467, CG13369, CG1544, CG32444, CG6910, CG9485, Gale, Galt, Gk, Hex-C, Sodh-1
GO:0016052	carbohydrate catabolic process	GO_BP	0.0348944	0.0000000	14.86	11	CG10467, CG13369, CG1544, CG32444, CG6910, CG9485, Gale, Galt, Gk, Hex-C, Sodh-1
R-DME:194002	Glucocorticoid biosynthesis	REACTOME	0.0355662	0.0000000	23.33	7	Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:194002	Glucocorticoid biosynthesis	REACTOME	0.0355662	0.0000235	23.33	7	Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0046514	ceramide catabolic process	GO_BP	0.0434632	0.0001275	50.00	4	CDase, CG31148, CG31414, CG7997
GO:0019388	galactose catabolic process	GO_BP	0.0434632	0.0000000	50.00	4	CG10467, CG32444, Gale, Galt
GO:0033499	galactose catabolic process via UDP-galactose	GO_BP	0.0434632	0.0000000	50.00	4	CG10467, CG32444, Gale, Galt
GO:0019388	galactose catabolic process	GO_BP	0.0434632	0.0000000	50.00	4	CG10467, CG32444, Gale, Galt
GO:0033499	galactose catabolic process via UDP-galactose	GO_BP	0.0434632	0.0000000	50.00	4	CG10467, CG32444, Gale, Galt
GO:0019388	galactose catabolic process	GO_BP	0.0434632	0.0000000	50.00	4	CG10467, CG32444, Gale, Galt
GO:0033499	galactose catabolic process via UDP-galactose	GO_BP	0.0434632	0.0000000	50.00	4	CG10467, CG32444, Gale, Galt
R-DME:140837	Intrinsic Pathway of Fibrin Clot Formation	REACTOME	0.0441913	0.0000000	22.58	7	Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:140875	Common Pathway of Fibrin Clot Formation	REACTOME	0.0441913	0.0000000	22.58	7	Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:140877	Formation of Fibrin Clot (Clotting Cascade)	REACTOME	0.0441913	0.0000000	22.58	7	Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:140837	Intrinsic Pathway of Fibrin Clot Formation	REACTOME	0.0441913	0.0000235	22.58	7	Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:140875	Common Pathway of Fibrin Clot Formation	REACTOME	0.0441913	0.0000235	22.58	7	Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
R-DME:140877	Formation of Fibrin Clot (Clotting Cascade)	REACTOME	0.0441913	0.0000235	22.58	7	Spn43Ab, Spn43Ad, Spn55B, Spn75F, Spn77Bb, Spn77Bc, Spn88Eb
GO:0016903	oxidoreductase activity, acting on the aldehyde or oxo group of donors	GO_MF	0.0444580	0.0000016	17.31	9	CG1544, CG17560, CG17562, CG18031, CG31076, CG4020, CG8665, CG9629, Fdh

This figure is related to Figure 3c

ClueGOResultTable_TDOWN_1.6_curr <- read.csv("Analysis/ClueGOResultTable_TDOWN_full_FC1.6_curated.csv",  header = TRUE, sep = ",")

ClueGOResultTable_TDOWN_1.6_curr <- as.data.frame(ClueGOResultTable_TDOWN_1.6_curr)
ClueGOResultTable_TDOWN_1.6_curr<- ClueGOResultTable_TDOWN_1.6_curr %>% arrange((Term_PValue_Corrected_with_Bonferroni_step_down)) # arrage the data how you want it in the plot 
ClueGOResultTable_TDOWN_1.6_curr<- ClueGOResultTable_TDOWN_1.6_curr %>% mutate(GOTerm = fct_reorder(GOTerm, desc(Term_PValue_Corrected_with_Bonferroni_step_down))) # lock in factor level order

ClueGOResultTable_TDOWN_1.6_curr_plot <- ggplot( ClueGOResultTable_TDOWN_1.6_curr, aes(x = -log10(Term_PValue_Corrected_with_Bonferroni_step_down), y = GOTerm, fill= OS_short)) + geom_bar(stat="identity", width=0.7 ) + scale_fill_brewer(palette="RdBu") +  theme_bw() + ylab(NULL) + xlab("-log10(term adjusted p value)") + theme(legend.position="right", text = element_text(size=15)) + geom_text(aes(label= Nr_Genes ), size=3, nudge_x = .7, color = "black" )  + scale_x_continuous(expand = c(0, 0), limits = c(0, 25)) + guides(fill=guide_legend(title="Ontology"))

ClueGOResultTable_TDOWN_1.6_curr_plot

 ggsave("1.6_figure_output/ClueGOResultTable_TDOWN_1.6_curr_plot.pdf", scale = 1, dpi = 320, width = 11, height = 6, limitsize = TRUE)

ClueGo results: Upregulated proteins

This table is related to Supplementary Table 9.

ClueGOResultTable_PUP_1.6 <- read.csv("Analysis/ClueGOResultTable_PUP_results.csv",  header = TRUE, sep = ",")
ClueGOResultTable_PUP_1.6 = ClueGOResultTable_PUP_1.6 %>% arrange(Term_PValue_Corrected_with_Bonferroni_step_down)

Table 13: ClueGO Results Table: Upregulated proteins

GO ID	GO Term	Ontology	Term P-value corrected	Group P-value corrected	% Associated Genes	No. Genes	Associated Genes
KEGG:00982	Drug metabolism	KEGG	0.0002751	0.0006024	8.82	6	CG5999, Fmo-1, GstD2, GstE5, GstE8, Ugt86Dd
KEGG:00980	Metabolism of xenobiotics by cytochrome P450	KEGG	0.0038868	0.0006024	7.25	5	CG5999, GstD2, GstE5, GstE8, Ugt86Dd
GO:0035009	Negative regulation of melanization defense response	GO_BP	0.0039896	0.0049293	66.67	2	Spn27A, Spn77Ba
KEGG:00983	Drug metabolism	KEGG	0.0166977	0.0006024	5.21	5	CG5999, GstD2, GstE5, GstE8, Ugt86Dd
R-DME:196071	Metabolism of steroid hormones	REACTOME	0.0269267	0.0049293	6.35	4	Cyp4ad1, Cyp4e3, Spn27A, Spn77Ba
R-DME:381119	Unfolded Protein Response	REACTOME	0.0319907	0.0058165	25.00	2	Ire1, PEK
GO:0006368	Transcription elongation from RNA polymerase II promoter	GO_BP	0.0347940	0.0347940	5.00	2	RpII15, atms
GO:0006414	Translational elongation	GO_BP	0.0390224	0.0039022	8.82	3	CG2017, Dgp-1, RpLP2
GO:0035007	Regulation of melanization defense response	GO_BP	0.0390736	0.0049293	22.22	2	Spn27A, Spn77Ba

This figure is related to Figure 3b

ClueGOResultTable_PUP_1.6_curr <- read.csv("Analysis/ClueGOResultTable_PUP_results_curated.csv",  header = TRUE, sep = ",")

ClueGOResultTable_PUP_1.6_curr <- as.data.frame(ClueGOResultTable_PUP_1.6_curr)
ClueGOResultTable_PUP_1.6_curr <- ClueGOResultTable_PUP_1.6_curr %>% arrange((Term_PValue_Corrected_with_Bonferroni_step_down)) # arrage the data how you want it in the plot 
ClueGOResultTable_PUP_1.6_curr <- ClueGOResultTable_PUP_1.6_curr %>% mutate(GOTerm = fct_reorder(GOTerm, desc(Term_PValue_Corrected_with_Bonferroni_step_down))) # lock in factor level order

ClueGOResultTable_PUP_1.6_curr_plot <- ggplot( ClueGOResultTable_PUP_1.6_curr, aes(x = -log10(Term_PValue_Corrected_with_Bonferroni_step_down), y = GOTerm, fill= OS_short)) + geom_bar(stat="identity", width=0.7 ) + scale_fill_brewer(palette="RdBu") +  theme_bw() + ylab(NULL) + xlab("-log10(term adjusted p value)") + theme(legend.position="right", text = element_text(size=15)) + geom_text(aes(label=No_Genes ), size=3, nudge_x = .7, color = "black" )  + scale_x_continuous(expand = c(0, 0), limits = c(0, 6)) + guides(fill=guide_legend(title="Ontology"))

ClueGOResultTable_PUP_1.6_curr_plot

ggsave("1.6_figure_output/ClueGOResultTable_PUP_1.6_curr_plot.pdf", scale = 1, dpi = 320, width = 11, height = 6, limitsize = TRUE)

ClueGo results: Downregulated proteins

This table is related to Supplementary Table 11.

ClueGOResultTable_PDOWN_1.6 <- read.csv("Analysis/ClueGOResultTable_PDOWN_results.csv",  header = TRUE, sep = ",")
ClueGOResultTable_PDOWN_1.6 = ClueGOResultTable_PDOWN_1.6 %>% arrange(Term_PValue_Corrected_with_Bonferroni_step_down)

Table 14: ClueGO Results Table: Downregulated proteins

GO ID	GO Term	Ontology	Term P-value corrected	Group P-value corrected	% Associated Genes	No. Genes	Associated Genes
GO:0005615	extracellular space	GO_CC	0.0000000	0.000000	4.47	33	Ag5r, CG14034, CG14661, CG16820, CG1701, CG17097, CG17242, CG18258, CG18284, CG31872, CG31883, CG34033, CG43319, CG4847, CG5162, CG6690, CG9029, CG9572, CecC, Cys, Dup99B, Est-6, Met75Ca, Obp51a, Sfp24Ba, Sfp24Bc, Sfp35C, Sfp60F, Spn28F, Spn75F, Spn77Bb, Spn77Bc, TotC
GO:0004866	endopeptidase inhibitor activity	GO_BP	0.0001106	0.000029	8.82	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0061135	endopeptidase regulator activity	GO_BP	0.0001290	0.000029	8.65	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0030414	peptidase inhibitor activity	GO_BP	0.0001384	0.000029	8.57	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0010951	negative regulation of endopeptidase activity	GO_BP	0.0001384	0.000029	8.57	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0010466	negative regulation of peptidase activity	GO_BP	0.0001736	0.000029	8.33	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0061134	peptidase regulator activity	GO_BP	0.0002329	0.000029	8.04	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
R-DME:196071	Metabolism of steroid hormones	REACTOME	0.0003627	0.000029	11.11	7	CG1444, Cyp4e1, Cyp4p1, Spn28F, Spn75F, Spn77Bb, Spn77Bc
R-DME:556833	Metabolism of lipids	REACTOME	0.0003800	0.000029	4.00	16	CG14034, CG1444, CG18258, CG1942, CG30008, CG3530, CG5162, Cyp4e1, Cyp4p1, Est-6, Spn28F, Spn75F, Spn77Bb, Spn77Bc, bgm, sigmar
GO:0045861	negative regulation of proteolysis	GO_BP	0.0004582	0.000029	7.38	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0004857	enzyme inhibitor activity	GO_BP	0.0013110	0.000029	6.47	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
R-DME:8939242	RUNX1 regulates transcription of genes involved in differentiation of keratinocytes	REACTOME	0.0013867	0.000029	16.13	5	CG4847, Spn28F, Spn75F, Spn77Bb, Spn77Bc
GO:0051346	negative regulation of hydrolase activity	GO_BP	0.0014375	0.000029	6.38	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0052548	regulation of endopeptidase activity	GO_BP	0.0014375	0.000029	6.38	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
R-DME:192456	Digestion of dietary lipid	REACTOME	0.0020873	0.001302	10.71	6	CG14034, CG17097, CG18258, CG18284, CG31872, CG5162
GO:0052547	regulation of peptidase activity	GO_BP	0.0020928	0.000029	6.08	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0004867	serine-type endopeptidase inhibitor activity	GO_BP	0.0024417	0.000029	8.24	7	CG16713, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc
R-DME:8853383	Lysosomal oligosaccharide catabolism	REACTOME	0.0031390	0.001999	42.86	3	LManIII, LManV, LManVI
GO:0004806	triglyceride lipase activity	GO_MF	0.0051737	0.001302	9.09	6	CG14034, CG17097, CG18258, CG18284, CG31872, CG5162
R-DME:8957322	Metabolism of steroids	REACTOME	0.0080892	0.000029	6.80	7	CG1444, Cyp4e1, Cyp4p1, Spn28F, Spn75F, Spn77Bb, Spn77Bc
R-DME:189200	Cellular hexose transport	REACTOME	0.0082248	0.000514	16.67	4	CG1208, CG14606, CG4607, CG6484
R-DME:1474290	Collagen formation	REACTOME	0.0088586	0.000029	10.87	5	CG4847, Spn28F, Spn75F, Spn77Bb, Spn77Bc
GO:0043086	negative regulation of catalytic activity	GO_BP	0.0091051	0.000029	4.97	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0006013	mannose metabolic process	GO_BP	0.0097572	0.001999	30.00	3	LManIII, LManV, LManVI
R-DME:8935690	Digestion	REACTOME	0.0113927	0.001302	7.79	6	CG14034, CG17097, CG18258, CG18284, CG31872, CG5162
GO:0005996	monosaccharide metabolic process	GO_BP	0.0148740	0.001999	7.41	6	Gbs-70E, Gnmt, LManIII, LManV, LManVI, smp-30
GO:0052689	carboxylic ester hydrolase activity	GO_MF	0.0154597	0.001302	5.19	8	CG14034, CG17097, CG18258, CG18284, CG31872, CG5162, Est-6, smp-30
GO:0005975	carbohydrate metabolic process	GO_BP	0.0166610	0.001999	3.79	11	Ald, Gbs-70E, Gnmt, LManIII, LManV, LManVI, Mal-A4, Mal-B1, Sodh-1, smp-30, tobi
R-DME:8963743	Digestion and absorption	REACTOME	0.0171912	0.001302	7.14	6	CG14034, CG17097, CG18258, CG18284, CG31872, CG5162
GO:0016836	hydro-lyase activity	GO_MF	0.0174234	0.001610	9.26	5	CG10424, CG3940, CG4594, CG6028, FASN3
R-DME:194002	Glucocorticoid biosynthesis	REACTOME	0.0176812	0.000029	13.33	4	Spn28F, Spn75F, Spn77Bb, Spn77Bc
R-DME:140837	Intrinsic Pathway of Fibrin Clot Formation	REACTOME	0.0198495	0.000029	12.90	4	Spn28F, Spn75F, Spn77Bb, Spn77Bc
R-DME:140875	Common Pathway of Fibrin Clot Formation	REACTOME	0.0198495	0.000029	12.90	4	Spn28F, Spn75F, Spn77Bb, Spn77Bc
R-DME:140877	Formation of Fibrin Clot (Clotting Cascade)	REACTOME	0.0198495	0.000029	12.90	4	Spn28F, Spn75F, Spn77Bb, Spn77Bc
GO:0044092	negative regulation of molecular function	GO_BP	0.0241268	0.000029	4.29	9	CG16713, Cys, Sfp24Ba, Sfp24Bc, Spn28F, Spn75F, Spn77Bb, Spn77Bc, sigmar
GO:0004559	alpha-mannosidase activity	GO_MF	0.0246031	0.001999	21.43	3	LManIII, LManV, LManVI
R-DME:3000178	ECM proteoglycans	REACTOME	0.0246642	0.000029	12.12	4	Spn28F, Spn75F, Spn77Bb, Spn77Bc
R-DME:375276	Peptide ligand-binding receptors	REACTOME	0.0269002	0.000029	11.76	4	Spn28F, Spn75F, Spn77Bb, Spn77Bc
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	GO_MF	0.0269177	0.001999	6.45	6	LManIII, LManV, LManVI, Mal-A4, Mal-B1, tobi
GO:0015923	mannosidase activity	GO_MF	0.0291322	0.001999	20.00	3	LManIII, LManV, LManVI
GO:0016835	carbon-oxygen lyase activity	GO_MF	0.0332794	0.001610	7.81	5	CG10424, CG3940, CG4594, CG6028, FASN3
R-DME:1650814	Collagen biosynthesis and modifying enzymes	REACTOME	0.0389050	0.000029	10.53	4	Spn28F, Spn75F, Spn77Bb, Spn77Bc
GO:0009410	response to xenobiotic stimulus	GO_BP	0.0478194	0.001621	16.67	3	CG17322, Cyp6t1, St3
GO:0006805	xenobiotic metabolic process	GO_BP	0.0478194	0.001621	16.67	3	CG17322, Cyp6t1, St3
GO:0071466	cellular response to xenobiotic stimulus	GO_BP	0.0478194	0.001621	16.67	3	CG17322, Cyp6t1, St3
GO:0016298	lipase activity	GO_MF	0.0481179	0.001302	5.71	6	CG14034, CG17097, CG18258, CG18284, CG31872, CG5162

This figure is related to Figure 3d

ClueGOResultTable_PDOWN_1.6_curr <- read.csv("Analysis/ClueGOResultTable_PDOWN_results_curated.csv",  header = TRUE, sep = ",")

ClueGOResultTable_PDOWN_1.6_curr <- as.data.frame(ClueGOResultTable_PDOWN_1.6_curr)
ClueGOResultTable_PDOWN_1.6_curr <- ClueGOResultTable_PDOWN_1.6_curr %>% arrange((Term_PValue_Corrected_with_Bonferroni_step_down)) # arrage the data how you want it in the plot 
ClueGOResultTable_PDOWN_1.6_curr<- ClueGOResultTable_PDOWN_1.6_curr %>% mutate(GOTerm = fct_reorder(GOTerm, desc(Term_PValue_Corrected_with_Bonferroni_step_down))) # lock in factor level order

ClueGOResultTable_PDOWN_1.6_curr_plot <- ggplot( ClueGOResultTable_PDOWN_1.6_curr, aes(x = -log10(Term_PValue_Corrected_with_Bonferroni_step_down), y = GOTerm, fill= OS_short)) + geom_bar(stat="identity", width=0.7 ) + scale_fill_brewer(palette="RdBu") +  theme_bw() + ylab(NULL) + xlab("-log10(term adjusted p value)") + theme(legend.position="right", text = element_text(size=15)) + geom_text(aes(label=No_Genes ), size=3, nudge_x = .7, color = "black" )  + scale_x_continuous(expand = c(0, 0), limits = c(0, 12)) + guides(fill=guide_legend(title="Ontology"))

ClueGOResultTable_PDOWN_1.6_curr_plot

ggsave("1.6_figure_output/ClueGOResultTable_PDOWN_1.6_curr_plot.pdf", scale = 1, dpi = 320, width = 11, height = 6, limitsize = TRUE)

ClueGo results: Upregulated transcripts and proteins (Group 1)

This table is related to Table 1

Table 16: Summary Table

webshot::install_phantomjs() # need this for save_kable

## phantomjs has been installed to /Users/rp636/Library/Application Support/PhantomJS

brief_summary <-  read.csv("1.6_data/Table1_Brief_summary.csv",  header = TRUE, sep = ",")
brief_summary2 <- brief_summary[c(2:5, 7:8, 10:17, 19:21, 23:24, 26:33), ]
write.csv(brief_summary2, "1.6_data_output/brief_summary2.csv") # need to remove the first column with numbers 
brief_summary3 <-  read.csv("1.6_data_output/brief_summary3.csv",  header = TRUE, sep = ",")

Summary <- kable(brief_summary3[, 1:4], booktabs = TRUE, col.names = gsub("[.]", " ", names(brief_summary3)), "html") %>% pack_rows(index = c("UPR-related molecules" = 4, "Translation" = 2 , "Detoxification" = 8, "Mitochondrial proteins" = 3, "Immunity-related proteins" = 2, "Other" = 7 )) %>% kable_styling(bootstrap_options = "striped", "scale_down", full_width = F, font_size = 10) %>% row_spec(0, font_size=11, bold = T) %>%
  kable_classic_2  %>% save_kable("1.6_figure_output/Summary.pdf")

## Note that HTML color may not be displayed on PDF properly.

## save_kable will have the best result with magick installed.

Gene name	Brief summary	Transcript FC	Protein FC
UPR-related molecules
PERK	UPR kinase	16.60	4.99
Sil1	Nucleotide exchange factor required for protein translocation and folding in the endoplasmic reticulum	8.58	1.80
AsnS	Asparagine synthase	4.30	2.30
Ire1	UPR kinase and endoribonuclease	2.09	1.71
Translation
Dgp-1	Translational GTPase predicted to be involved in translational elongation	21.20	2.30
CG2017	Translational GTPase predicted to be involved in translational elongation	2.60	1.69
Detoxification
Cyp6a17	Cytochrome P450 enzyme	117.00	19.03
Cyp9b2	Cytochrome P450 enzyme	6.96	2.28
Cyp4e3	Cytochrome P450 enzyme	3.22	2.97
Cyp4ad1	Cytochrome P450 enzyme	1.61	1.72
Ugt37A3	UDP-glycosyltransferase	69.40	13.27
Ugt86Dd	UDP-glycosyltransferase	3.48	3.34
GstD2	Glutathione S transferase	7.49	3.68
GstE8	Glutathione S transferase	2.70	2.08
Mitochondrial proteins
Hsp22	Mitochondrial molecular chaperone	29.20	28.25
Pepck2	Mitochondrial and cytoplasmic phosphoenolpyruvate carboxykinase, plays a role in gluconeogenesis	2.63	1.65
CG34423	Mitochondrial ATPase inhibitor	2.40	1.96
Immunity-related proteins
Lectin-galC1	Galactose binding protein involved in the induction of bacterial agglutination and cell-cell adhesion	3.26	9.71
BomBc3	Member of the Bombamin family of small, secreted immune-induced peptides that are induced by Toll signalling and may function to confer resistance to bacterial infection	2.56	3.92
Other
CG11911	Predicted to have serine-type endopeptidase activity and be involved in proteolysis	6.96	9.32
Uro	Urate oxidase, involved in allantoin biosynthetic process	3.73	1.79
Ccp84Ab	Predicted to be a structural constituent of chitin-based larval cuticle	1.92	1.77
CG17752	A member of the Solute carrier family 22 (SLC22), predicted to have transmembrane transporter activity	1.80	1.73
CG7632	Predicted to have hydrolase activity	3.57	1.95
CG43402	Uncharacterized protein	6.77	2.20
CG12868	Uncharacterized protein	2.17	2.36
CG31808	Uncharacterized protein	1.84	2.62

ClueGo results: Upregulated transcripts and no change in proteins (Group 2)

ClueGO: Molecular Function & Biological Process

This table is related to Supplementary Table 20 .

ClueGOResultTable_raw_TUP_PZERO_1.6 <- read.csv("Analysis/ClueGOResultTable_TUP_PZERO_1.6_R.csv",  header = TRUE, sep = ",")

Table 17: ClueGO Results Table: Upregulated transcripts and no change in proteins

GO ID	GO Term	Ontology	Term P-value corrected	Group P-value corrected	% Associated Genes	No. Genes	Associated Genes
GO:0015695	Organic cation transport	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0018548	0.0006451	25.00	3	CG3476, Orct2, Tpc1
GO:0097190	Apoptotic signaling pathway	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0422428	0.0253457	5.26	3	CG5059, Dronc, Rbf
KEGG:00270	Cysteine and methionine metabolism	KEGG_15.01.2021	0.0028284	0.0009428	11.11	4	CG1461, CG1673, Gclc, ImpL3
GO:0001666	Response to hypoxia	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0362782	0.0147623	4.62	3	Drat, eIF2B-gamma, l(2)37Cc
GO:0036293	Response to decreased oxygen levels	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0147623	0.0147623	4.29	3	Drat, eIF2B-gamma, l(2)37Cc
R-DME:1362409	Mitochondrial iron-sulfur cluster biogenesis	REACTOME_Pathways_15.01.2021	0.0014593	0.0082155	27.27	3	CG12264, Fdx2, bcn92
GO:0051536	Iron-sulfur cluster binding	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0252045	0.0082155	4.55	3	CG12264, Fdx2, FeCH
KEGG:00240	Pyrimidine metabolism	KEGG_15.01.2021	0.0343269	0.0262478	7.50	3	CG16758, NTPase, l(2)k01209
R-DME:15869	Metabolism of nucleotides	REACTOME_Pathways_15.01.2021	0.0393091	0.0262478	5.77	3	CG16758, NTPase, l(2)k01209
R-DME:8949215	Mitochondrial calcium ion transport	REACTOME_Pathways_15.01.2021	0.0022941	0.0054885	23.08	3	CG2658, CG6512, l(2)37Cc
R-DME:8949664	Processing of SMDT1	REACTOME_Pathways_15.01.2021	0.0007822	0.0054885	33.33	3	CG2658, CG6512, l(2)37Cc
GO:0007006	Mitochondrial membrane organization	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0411042	0.0054885	6.00	3	CG2658, CG5059, CG6512
GO:0004497	Monooxygenase activity	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0056805	0.0071724	4.84	6	Cyp28a5, Cyp309a1, Cyp6a20, Cyp6a22, Cyp6a23, Cyp9b1
GO:0046906	Tetrapyrrole binding	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0123261	0.0071724	4.00	6	Cyp28a5, Cyp309a1, Cyp6a20, Cyp6a22, Cyp6a23, Cyp9b1
GO:0020037	Heme binding	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0126962	0.0071724	4.03	6	Cyp28a5, Cyp309a1, Cyp6a20, Cyp6a22, Cyp6a23, Cyp9b1
GO:0005506	Iron ion binding	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0038858	0.0071724	4.29	7	CG30022, Cyp28a5, Cyp309a1, Cyp6a20, Cyp6a22, Cyp6a23, Cyp9b1
KEGG:00480	Glutathione metabolism	KEGG_15.01.2021	0.0000506	0.0000107	8.86	7	Gclc, GstD3, GstD9, GstE1, GstE7, GstE9, GstT1
KEGG:00980	Metabolism of xenobiotics by cytochrome P450	KEGG_15.01.2021	0.0000214	0.0000107	10.14	7	GstD3, GstD9, GstE1, GstE7, GstE9, GstT1, Ugt36Bc
KEGG:00982	Drug metabolism	KEGG_15.01.2021	0.0000199	0.0000107	10.29	7	GstD3, GstD9, GstE1, GstE7, GstE9, GstT1, Ugt36Bc
KEGG:00983	Drug metabolism	KEGG_15.01.2021	0.0000163	0.0000107	8.33	8	GstD3, GstD9, GstE1, GstE7, GstE9, GstT1, Ugt36Bc, l(2)k01209
GO:0006790	Sulfur compound metabolic process	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0000330	0.0000107	5.35	10	CG12264, CG30022, Gclc, GstD3, GstD9, GstE1, GstE7, GstE9, GstT1, bcn92
GO:0016765	Transferase activity, transferring alkyl or aryl (other than methyl) groups	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0002397	0.0000107	9.09	6	GstD3, GstD9, GstE1, GstE7, GstE9, GstT1
GO:0006575	Cellular modified amino acid metabolic process	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0000010	0.0000107	9.47	9	CG30022, Gclc, GstD3, GstD9, GstE1, GstE7, GstE9, GstT1, Nmdmc
GO:0004364	Glutathione transferase activity	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0000143	0.0000107	15.00	6	GstD3, GstD9, GstE1, GstE7, GstE9, GstT1
GO:0006749	Glutathione metabolic process	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0000002	0.0000107	14.55	8	CG30022, Gclc, GstD3, GstD9, GstE1, GstE7, GstE9, GstT1
GO:0016875	Ligase activity, forming carbon-oxygen bonds	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0348229	0.0000005	7.69	3	Aats-thr, CG10802, CG17259
GO:0070279	Vitamin B6 binding	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0350078	0.0000005	7.89	3	CG12264, CG1461, CG3999
GO:0004812	Aminoacyl-tRNA ligase activity	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0348229	0.0000005	7.69	3	Aats-thr, CG10802, CG17259
GO:0006520	Cellular amino acid metabolic process	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0002844	0.0000005	4.71	9	Aats-thr, CG10802, CG11796, CG1461, CG1673, CG17259, CG3999, Ppn, aay
GO:0030170	Pyridoxal phosphate binding	GO_MolecularFunction-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0350078	0.0000005	7.89	3	CG12264, CG1461, CG3999
GO:0043038	Amino acid activation	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0368601	0.0000005	6.82	3	Aats-thr, CG10802, CG17259
GO:1901605	Alpha-amino acid metabolic process	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0284431	0.0000005	4.10	5	CG11796, CG1461, CG3999, Ppn, aay
GO:0009063	Cellular amino acid catabolic process	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0463814	0.0000005	4.69	3	CG1461, CG3999, Ppn
GO:0009069	Serine family amino acid metabolic process	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0072076	0.0000005	15.00	3	CG3999, Ppn, aay
GO:1901606	Alpha-amino acid catabolic process	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0119169	0.0000005	7.27	4	CG11796, CG1461, CG3999, Ppn
GO:0043039	tRNA aminoacylation	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0334922	0.0000005	7.32	3	Aats-thr, CG10802, CG17259
GO:0006399	tRNA metabolic process	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0002689	0.0000005	5.59	8	Aats-thr, CG10802, CG12264, CG17259, CG4611, CG9987, Elp1, Rrp42
GO:0006418	tRNA aminoacylation for protein translation	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0348229	0.0000005	7.69	3	Aats-thr, CG10802, CG17259
GO:0008033	tRNA processing	GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0434607	0.0000005	4.17	4	CG12264, CG4611, CG9987, Elp1

This figure is related to Figure 7 (left)

ClueGOResultTable_TUP_PZERO_1.6 <- read.csv("Analysis/ClueGOResultTable_TUP_PZERO_1.6_curated.csv",  header = TRUE, sep = ",")

ClueGOResultTable_TUP_PZERO_1.6 <- as.data.frame(ClueGOResultTable_TUP_PZERO_1.6)
ClueGOResultTable_TUP_PZERO_1.6 <- ClueGOResultTable_TUP_PZERO_1.6 %>% arrange((Term_Pvalue_Corrected_with_Bonferroni_step_down)) # arrage the data how you want it in the plot 
ClueGOResultTable_TUP_PZERO_1.6 <- ClueGOResultTable_TUP_PZERO_1.6 %>% mutate(GOTerm = fct_reorder(GOTerm, desc(Term_Pvalue_Corrected_with_Bonferroni_step_down))) # lock in factor level order

ClueGOResultTable_TUP_PZERO_1.6_plot <- ggplot( ClueGOResultTable_TUP_PZERO_1.6, aes(x = -log10(Term_Pvalue_Corrected_with_Bonferroni_step_down), y = GOTerm, fill= OS_short)) + geom_bar(stat="identity", width=0.7 ) + scale_fill_brewer(palette="RdBu") +  theme_bw() + ylab(NULL) + xlab("-log10(term adjusted p value)") + theme(legend.position="right", text = element_text(size=15)) + geom_text(aes(label=No_Genes ), size=3, nudge_x = .7, color = "black" )  + scale_x_continuous(expand = c(0, 0), limits = c(0, 8)) + guides(fill=guide_legend(title="Ontology"))

ClueGOResultTable_TUP_PZERO_1.6_plot

ggsave("1.6_figure_output/ClueGOResultTable_TUP_PZERO_1.6_plot.pdf", scale = 1, dpi = 320, width = 9, limitsize = TRUE)

## Saving 9 x 5 in image

ClueGO: Cellular component

This table is related to Supplementary Table 19.

ClueGOResultTable_GOCC_TUP_PZERO_1.6 <- read.csv("Analysis/ClueGOResultTable_GOCC_TUP_PZERO_1.6_R.csv",  header = TRUE, sep = ",")

## Warning in read.table(file = file, header = header, sep = sep, quote =
## quote, : incomplete final line found by readTableHeader on 'Analysis/
## ClueGOResultTable_GOCC_TUP_PZERO_1.6_R.csv'

Table 18: ClueGO Results Table: GO Cellular Component: Upregulated transcripts and no change in proteins

GO ID	GO Term	Ontology	Term P-value corrected	Group P-value corrected	% Associated Genes	No. Genes	Associated Genes
GO:0005739	mitochondrion	GO_CellularComponent-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0000640	0.0000427	2.11	20	Aats-thr, Alr, CG12264, CG1673, CG2658, CG30022, CG3476, CG3999, CG4611, CG5059, CG6512, Fdx2, FeCH, Nmdmc, Ppn, Tpc1, bcn92, l(2)37Cc, mRpS31, mtSSB
GO:0019866	organelle inner membrane	GO_CellularComponent-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0176714	0.0088357	2.27	7	CG2658, CG3476, CG6512, FeCH, Tpc1, bocks, l(2)37Cc
GO:0005743	mitochondrial inner membrane	GO_CellularComponent-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00	0.0234936	0.0088357	2.05	6	CG2658, CG3476, CG6512, FeCH, Tpc1, l(2)37Cc

This figure is related to Figure 7 (left)

ClueGOResultTable_GOCC_TUP_PZERO_1.6_curr <- read.csv("Analysis/ClueGOResultTable_GOCC_TUP_PZERO_1.6_curated.csv",  header = TRUE, sep = ",")

## Warning in read.table(file = file, header = header, sep = sep, quote =
## quote, : incomplete final line found by readTableHeader on 'Analysis/
## ClueGOResultTable_GOCC_TUP_PZERO_1.6_curated.csv'

ClueGOResultTable_GOCC_TUP_PZERO_1.6_plot <- ggplot( ClueGOResultTable_GOCC_TUP_PZERO_1.6_curr, aes(x = -log10(Term_Pvalue_Corrected_with_Bonferroni_step_down), y = GOTerm, fill= GOTerm)) + geom_bar(stat="identity", width=0.7 ) + scale_fill_brewer(palette="Set1") +  theme_bw() + ylab(NULL) + xlab("-log10(term adjusted p value)") + theme(legend.position="none", text = element_text(size=20)) + geom_text(aes(label=No_Genes ), size=6, nudge_x = .7, color = "black" )  + scale_x_continuous(expand = c(0, 0), limits = c(0, 8)) + theme(axis.text.y = element_text(face = "plain", colour = "black"))

ClueGOResultTable_GOCC_TUP_PZERO_1.6_plot

ggsave("1.6_figure_output/ClueGOResultTable_GOCC_TUP_PZERO_1.6_plot.pdf", scale = 1, dpi = 320, width = 9, limitsize = TRUE)

## Saving 9 x 5 in image

Looking into mitochondrial genes (from FlyBase unless otherwise specified)

• I also found some additional mitochondrial genes (or at least thought of as mitochondrial or related to mitochondrial function) not picked up by this analysis.

• TPC1: Thiamine pyrophosphate carrier protein 1 (Tpc1) encodes an important protein for mitochondrial metabolism located at the inner mitochondrial membrane. Exhibits antiporter activity and thiamine transmembrane transporter activity. Its main role is to import thiamine pyrophosphate (ThPP) into mitochondria. ThPP is an essential coenzyme for the E1 components of pyruvate dehydrogenase and oxoglutarate dehydrogenase, which are located in the mitochondrial matrix. Orthologous to human SLC25A19 (solute carrier family 25 member 19).The solute carrier family 25 (SLC25) or mitochondrial carrier family (MCF) members shuttle metabolites, nucleotides and cofactors across the inner mitochondrial membrane. (Adapted from FBrf0212481, FBrf0212949 and PMID:23266187).

• CG4611: Predicted to have RNA binding activity. Predicted to be involved in tRNA 3’-end processing. Predicted to localize to mitochondrion. Orthologous to several human genes including PTCD1 (pentatricopeptide repeat domain 1). Mammalian PTCD1 was shown to be required for the proper assembly of the ETC. Loss of PTCD1 function strongly diminishes energy generation by mitochondria, forcing cells to rely on glycolysis (Fleck et al., 2019).

• CG30022: Predicted to have hydrolase activity, acting on ester bonds; iron ion binding activity; and sulfur dioxygenase activity. Predicted to be involved in glutathione metabolic process and hydrogen sulfide metabolic process. Predicted to localize to mitochondrion and nucleoplasm. Human ortholog(s) of this gene implicated in ethylmalonic encephalopathy. Orthologous to human ETHE1 (ETHE1 persulfide dioxygenase) (FlyBase). This gene encodes a member of the metallo beta-lactamase family of iron-containing proteins involved in the mitochondrial sulfide oxidation pathway. The encoded protein catalyzes the oxidation of a persulfide substrate to sulfite (Entrez Gene Summary for ETHE1 Gene). Sulfur dioxygenase that plays an essential role in hydrogen sulfide catabolism in the mitochondrial matrix. Hydrogen sulfide (H(2)S) is first oxidized by SQRDL, giving rise to cysteine persulfide residues. ETHE1 consumes molecular oxygen to catalyze the oxidation of the persulfide, once it has been transferred to a thiophilic acceptor, such as glutathione (R-SSH). Plays an important role in metabolic homeostasis in mitochondria by metabolizing hydrogen sulfide and preventing the accumulation of supraphysiological H(2)S levels that have toxic effects, due to the inhibition of cytochrome c oxidase (UniProtKB/Swiss-Prot Summary for ETHE1 Gene).

• FECH: Ferrochelatase. Ferrochelatases catalyze the synthesis of protoheme by inserting ferrous iron into the protoporphyrin. Predicted to be involved in protoporphyrinogen IX biosynthetic process. Predicted to localize to mitochondrial inner membrane. Is expressed in several structures, including adult head; adult heart; embryonic/larval midgut; embryonic/larval muscle system; and presumptive embryonic/larval digestive system. Human ortholog(s) of this gene implicated in cutaneous porphyria and erythropoietic protoporphyria. Orthologous to human FECH (ferrochelatase). Last step of Heme Biosynthesis.

• L(2)37CC: nvolved in cellular response to hypoxia. Localizes to mitochondrion. Is expressed in several structures, including embryonic/larval muscle system; extended germ band embryo; gut section; spermatozoon; and visceral muscle primordium. Human ortholog(s) of this gene implicated in breast cancer and sporadic breast cancer. Orthologous to human PHB (prohibitin). Required for larval metabolism or for the progression of the larva into a pupa (FlyBase). Mammalian prohibitin is evolutionarily conserved, and its product is proposed to play a role in human cellular senescence and tumor suppression. Antiproliferative activity is reported to be localized to the 3’ UTR, which is proposed to function as a trans-acting regulatory RNA. Several pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants (Entrez Gene Summary for PHB Gene). Regulates mitochondrial respiration activity and in aging (PubMed:11302691). In neurons, regulates the protein turnover of OMA1 in a cardiolipin-binding manner (By similarity). Inhibits DNA synthesis (By similarity) (UniProtKB/Swiss-Prot Summary for PHB Gene).

• CG6512: Predicted to have metalloendopeptidase activity. ATP-dependent metalloendopeptidases belong to MEROPS family M41 and catalyse the hydrolysis of proteins in the presence of ATP. They are localized to mitochondria and are involved in protein turnover and respiratory chain complex assembly. Predicted to be involved in mitochondrial protein processing; mitochondrion organization; and protein-containing complex assembly. Predicted to localize to mitochondrial inner membrane. Is expressed in several structures, including anterior endoderm; anterior endoderm anlage; embryonic/larval muscle system; extended germ band embryo; and gut section. Human ortholog(s) of this gene implicated in optic atrophy; spastic ataxia; spastic ataxia 5; and spinocerebellar ataxia type 28. Orthologous to human AFG3L2 (AFG3 like matrix AAA peptidase subunit 2). ts molecular function is described by: zinc ion binding; metalloendopeptidase activity; ATP binding. It is involved in the biological process described with: mitochondrial protein processing; mitochondrial fusion; proteolysis; cristae formation; protein-containing complex assembly. 8 alleles are reported. Human AFG3L2 is an ATP-dependent protease which is essential for axonal and neuron development. In neurons, mediates degradation of SMDT1/EMRE before its assembly with the uniporter complex, limiting the availability of SMDT1/EMRE for MCU assembly and promoting efficient assembly of gatekeeper subunits with MCU (PubMed:27642048). Required for the maturation of paraplegin (SPG7) after its cleavage by mitochondrial-processing peptidase (MPP), converting it into a proteolytically active mature form (By similarity). Required for the maturation of PINK1 into its 52kDa mature form after its cleavage by mitochondrial-processing peptidase (MPP) (PubMed:22354088) (UniProtKB).

• THRRS (Aats-thr): Threonyl-tRNA synthetase. Predicted to have threonine-tRNA ligase activity. Predicted to be involved in threonyl-tRNA aminoacylation. Dual-localized aminoacyl-tRNA synthetases are encoded by single genes and catalyze the ligation of amino acids to their cognate tRNAs in the cytoplasmic and mitochondrial compartments (Adapted from FBrf0230668.). Aminoacyl-tRNA editing hydrolases catalyze the hydrolysis of an incorrectly aminoacylated tRNA. Predicted to localize to mitochondrion. Is expressed in several structures, including anterior endoderm anlage; embryonic/larval digestive system; embryonic/larval muscle system; germ layer; and presumptive embryonic/larval digestive system. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 21 and nonphotosensitive trichothiodystrophy 7. Orthologous to several human genes including TARS3 (threonyl-tRNA synthetase 3). Its molecular function is described by: ATP binding; aminoacyl-tRNA editing activity; threonine-tRNA ligase activity. It is involved in the biological process described with: threonyl-tRNA aminoacylation.

• CG3476: Mitochondrial Magnesium Exporter 1 (MME1). Exhibits magnesium ion transmembrane transporter activity. Involved in cellular magnesium ion homeostasis and magnesium ion export from mitochondrion. Predicted to localize to mitochondrial inner membrane. Is expressed in several structures, including adult head; anterior endoderm anlage; embryonic/larval midgut; embryonic/larval midgut primordium; and posterior endoderm. Human ortholog(s) of this gene implicated in carnitine-acylcarnitine translocase deficiency. Orthologous to human SLC25A20 (solute carrier family 25 member 20). The solute carrier family 25 (SLC25) or mitochondrial carrier family (MCF) members shuttle metabolites, nucleotides and cofactors across the inner mitochondrial membrane. (Adapted from FBrf0212481, FBrf0212949 and PMID:23266187). Its molecular function is described by: carnitine:acyl carnitine antiporter activity; magnesium ion transmembrane transporter activity. It is involved in the biological process described with 6 unique terms, many of which group under: cation transport; transport; nitrogen compound transport; establishment of localization; organic cation transport.

• CG2658: Spg7 or Paraplegin. Predicted to have ATPase activity and metallopeptidase activity. ATP-dependent metalloendopeptidases belong to MEROPS family M41 and catalyse the hydrolysis of proteins in the presence of ATP. They are localized to mitochondria and are involved in protein turnover and respiratory chain complex assembly. Predicted to be involved in mitochondrial protein processing; mitochondrion organization; and protein-containing complex assembly. Localizes to mitochondrion. Is expressed in adult head and spermatozoon. Used to study hereditary spastic paraplegia 7. Human ortholog(s) of this gene implicated in hereditary spastic paraplegia 7. Orthologous to human SPG7 (SPG7 matrix AAA peptidase subunit, paraplegin). Its molecular function is described by: ATPase activity; metalloendopeptidase activity; ATP binding; metallopeptidase activity; zinc ion binding. It is involved in the biological process described with: mitochondrial fusion; mitochondrial protein processing; proteolysis; cristae formation; protein-containing complex assembly.

• CG12264: Nfs1 cysteine desulfurase. Exhibits cysteine desulfurase activity. Involved in iron-sulfur cluster assembly. Localizes to L-cysteine desulfurase complex and nucleus. Is expressed in adult head; adult heart; embryonic/larval midgut; embryonic/larval visceral muscle; and organism. Orthologous to human NFS1 (NFS1 cysteine desulfurase).Sulfurtransferases catalyze the transfer of sulfur-containing groups.Catalyzes the removal of elemental sulfur from cysteine to produce alanine. It supplies the inorganic sulfur for iron-sulfur (Fe-S) clusters.

• BCN92: Involved in iron-sulfur cluster assembly. Localizes to L-cysteine desulfurase complex and mitochondrion. Is expressed in adult head. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 19. Orthologous to human LYRM4 (LYR motif containing 4). Interacts with Nfs1 (Marelja et al., 2018, Guruharsha et al., 2011).

• ALR: Augmenter of liver regeneration. Predicted to have flavin adenine dinucleotide binding activity; flavin-linked sulfhydryl oxidase activity; and protein disulfide oxidoreductase activity. Involved in tissue regeneration. Predicted to localize to mitochondrion. Is expressed in adult head; ectoderm; organism; and prothoracic leg disc. Human ortholog(s) of this gene implicated in kidney failure and renal fibrosis. Orthologous to human GFER (growth factor, augmenter of liver regeneration). Sulfur oxidoreductases with oxygen as acceptor, include dehydrogenases that oxidize sulfur-containing group with the reduction of oxygen molecule. Disulfide oxidoreductases include dehydrogenases that catalyze the oxidation of substrate with reduced sulfide groups into substrate with oxidized disulfide bonds.

• CG40002: ND-AGGG. NADH dehydrogenase (ubiquinone) AGGG subunit. Predicted to localize to mitochondrial respiratory chain complex I (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2). Is expressed in adult head and adult heart. Mitochondrial Complex I is the first and largest holoenzyme of the mitochondrial electron transport chain. It oxidizes NADH from the tricarboxylic acid cycle and β oxidation of fatty acids, reduces ubiquinone and transports protons across the inner membrane, contributing to the proton-motive force. It is also involved in the cellular production of reactive oxygen species. ‘Accessory’ or ‘supernumerary’ subunits are all encoded by nuclear DNA and are not directly involved in catalysis.

• NMDMC: NAD-dependent methylenetetrahydrofolate dehydrogenase. Predicted to have several functions, including magnesium ion binding activity; methenyltetrahydrofolate cyclohydrolase activity; and methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity. Predicted to be involved in 10-formyltetrahydrofolate metabolic process; carbohydrate metabolic process; and tetrahydrofolate interconversion. Predicted to localize to mitochondrion. Is expressed in adult head; amnioserosa; embryonic rectum; rectum primordium; and yolk nucleus. Orthologous to human MTHFD2L (methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2 like) and MTHFD2 (methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase). CH-NH oxidoreductases with NAD or NADP as acceptor, include dehydrogenases that oxidize a CH-NH with the reduction of NAD or NADP. Other Carbon-Nitrogen hydrolases of cyclic amidines are a collection of Carbon-Nitrogen hydrolases of cyclic amidines that do not fit into any other major hydrolases.ATF4-dependant target.

• CG5059: BNIP3. Predicted to be involved in mitochondrial outer membrane permeabilization and regulation of programmed cell death. Localizes to nucleus. Is expressed in several structures, including adult head; apoptotic amnioserosa; ectoderm; ectoderm anlage; and extended germ band embryo. Orthologous to several human genes including BNIP3 (BCL2 interacting protein 3).

• MRPS31: Mitochondrial ribosomal protein S31.Mitochondrial 28S ribosomal protein S31. Predicted to be a structural constituent of ribosome. Predicted to be involved in translation. Predicted to localize to mitochondrial small ribosomal subunit. Is expressed in several structures, including adult head; embryonic/larval muscle system; extended germ band embryo; gut section; and spermatozoon. Orthologous to human MRPS31 (mitochondrial ribosomal protein S31). Mitochondrial ribosomes are found in the mitochondrial matrix and translate genes involved in oxidative phosphorylation encoded by the mitochondrial genome. Ribosomes are formed by two ribonucleoprotein subunits, large and small. The principle function of the small subunit is to bind mRNA. (Adapted from FBrf0205398).

• CG1319: Fdx2. Ferredoxin 2. Predicted to have electron transfer activity. Involved in positive regulation of ecdysteroid biosynthetic process. Predicted to localize to mitochondrial matrix. Is expressed in several structures, including adult heart; gut section; posterior endoderm; and presumptive embryonic/larval digestive system. Orthologous to human FDX1 (ferredoxin 1). The Other oxidoreductases, is a collection of oxidoreductases that do not fit into any of the other major oxidoreductases. Required for ecdysteroidogenesis in the prothoracic gland which is necessary for larval to pupal transition.

• MTSSB: Mitochondrial single stranded DNA-binding protein. Exhibits single-stranded DNA binding activity. Involved in several processes, including DNA replication; positive regulation of exodeoxyribonuclease activity; and regulation of DNA-dependent DNA replication. Localizes to mitochondrial chromosome. Is expressed in several structures, including adult heart; embryonic/larval midgut; embryonic/larval midgut primordium; ovary; and wing disc. Orthologous to human SSBP1 (single stranded DNA binding protein 1). Binds preferentially and cooperatively to pyrimidine rich single-stranded DNA (ss-DNA) (PubMed:7673145, PubMed:8206370, PubMed:21953457). Required to maintain the copy number of mitochondrial DNA (mtDNA) and plays crucial roles during mtDNA replication that stimulate activity of the gamma complex polymerase tam at the replication fork (PubMed:21953457, PubMed:26446790, PubMed:14754882, PubMed:28318978, PubMed:7673145, PubMed:11294889). Promotes tam activity largely by organizing the template DNA and eliminating secondary structures to favor ss-DNA conformations that facilitate tam activity (PubMed:26446790, PubMed:21953457, PubMed:7673145).

• CG3999: Predicted to have glycine binding activity; glycine dehydrogenase (decarboxylating) activity; and pyridoxal phosphate binding activity. Predicted to be involved in glycine decarboxylation via glycine cleavage system. Predicted to localize to glycine cleavage complex and mitochondrion. Is expressed in adult head; adult heart; embryonic/larval fat body; fat body/gonad primordium; and yolk nucleus. Human ortholog(s) of this gene implicated in glycine encephalopathy. Orthologous to human GLDC (glycine decarboxylase). CH-NH2 oxidoreductases with disulfide as acceptor, include dehydrogenases that oxidize a CH-NH2 group with the reduction of disulfide group.

• CG1673 Predicted to have branched-chain-amino-acid transaminase activity. Predicted to be involved in leucine biosynthetic process and valine biosynthetic process. Predicted to localize to mitochondrion. Is expressed in adult head and spermatozoon. Orthologous to human BCAT1 (branched chain amino acid transaminase 1) and BCAT2 (branched chain amino acid transaminase 2). Transaminases catalyze the interconversion of amino acids and oxoacids by transfer of amino groups.

• Puml Pummelig. Exhibits carboxylic ester hydrolase activity. Predicted to be involved in lipid homeostasis and phosphatidic acid biosynthetic process. Predicted to localize to lipid droplet; mitochondrion; and peroxisome. Is expressed in several structures, including embryonic/larval fat body; embryonic/larval midgut primordium; embryonic/larval posterior spiracle; germ layer; and spermatozoon. Used to study obesity. Human ortholog(s) of this gene implicated in autosomal recessive congenital ichthyosis 1 and neutral lipid storage disease. Orthologous to human ABHD4 (abhydrolase domain containing 4, N-acyl phospholipase B) and ABHD5 (abhydrolase domain containing 5, lysophosphatidic acid acyltransferase). Its molecular function is described by: carboxylic ester hydrolase activity; lysophosphatidic acid acyltransferase activity. OTHER CARBOXYLESTERASES are carboxylesterases that do not fall into any other major carboxylesterase group. The other lysophospholipid acyltransferases are a collection of transferases that do not fit into any of the other major lysophospholipid acyltransferases.

• Dronc Death regulator Nedd2-like caspase (Dronc) encodes an initiator caspase that is essential for caspase-dependent cell death. It is also implicated in the DNA damage response, sperm differentiation and cell specification. Exhibits cysteine-type endopeptidase activity involved in apoptotic signaling pathway and protein homodimerization activity. Involved in several processes, including positive regulation of cell death; programmed cell death involved in cell development; and protein processing. Localizes to apoptosome; nucleus; and plasma membrane. Is expressed in several structures, including extended germ band embryo; eye disc; foregut primordium; germline cyst; and gut section. Used to study testicular cancer. Orthologous to human CASP2 (caspase 2). The apoptosome is a ring-like multisubunit complex assembled upon receiving a pro-apoptotic signal. In Drosophila, Dark assembles into two stacked rings of eight subunits each. This scaffold binds ADP and an initiator caspase (Dronc in D.mel) which cleaves effector caspase(s). Involved in the activation cascade of caspases responsible for apoptosis execution. Effector of steroid-mediated apoptosis during insect metamorphosis. Overexpression promotes programmed cell death. Interaction with Diap1 is required to suppress Dronc-mediated cell death; via Diap1-mediated ubiquitination of Dronc. Rate-limiting caspase in rpr and hid death pathway. Cysteine protease - a functional homolog of CED-3/caspase-9 - initiator caspase - involved in programmed cell death - activated by interaction with the Apaf-containing apoptosome

• CG10924 Pepck2. Phosphoenolpyruvate carboxykinase 2. Predicted to have manganese ion binding activity and phosphoenolpyruvate carboxykinase (GTP) activity. Predicted to be involved in several processes, including cellular response to glucose stimulus; gluconeogenesis; and monocarboxylic acid metabolic process. Predicted to localize to cytosol and mitochondrion. Is expressed in several structures, including embryonic/larval midgut primordium; extended germ band embryo; gastrula embryo; posterior ectoderm anlage; and yolk. Orthologous to human PCK2 (phosphoenolpyruvate carboxykinase 2, mitochondrial). Carboxy-lyases are involved in the the addition of a carboxyl group to a compound (carboxylases) or the removal of a carboxyl group from a compound (decarboxylases).

ClueGo results: Downregulated transcripts and proteins

ClueGO: Molecular Function & Biological Process

This table is related to Supplementary Table 21 .

ClueGOResultTable_TDOWN_PDOWN_1.6 <- read.csv("Analysis/TDOWN_PDOWN_ClueGOResultTable_detail.csv",  header = TRUE, sep = ",")

Table 18: ClueGO Results Table: Downregulated transcripts and proteins

GO ID	GO Term	Ontology	Term P-value corrected	Group P-value corrected	% Associated Genes	No. Genes	Associated Genes
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	GO_MF	0.0000368	0.0000011	6.45	6	LManIII, LManV, LManVI, Mal-A4, Mal-B1, tobi
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	GO_MF	0.0000368	0.0000037	6.45	6	LManIII, LManV, LManVI, Mal-A4, Mal-B1, tobi
R-DME:8853383	Lysosomal oligosaccharide catabolism	REACTOME	0.0000599	0.0000011	42.86	3	LManIII, LManV, LManVI
R-DME:8853383	Lysosomal oligosaccharide catabolism	REACTOME	0.0000599	0.0000037	42.86	3	LManIII, LManV, LManVI
R-DME:8939242	RUNX1 regulates transcription of genes involved in differentiation of keratinocytes	REACTOME	0.0001647	0.0075793	12.90	4	CG4847, Spn75F, Spn77Bb, Spn77Bc
GO:0006013	mannose metabolic process	GO_BP	0.0001940	0.0000011	30.00	3	LManIII, LManV, LManVI
GO:0006013	mannose metabolic process	GO_BP	0.0001940	0.0000037	30.00	3	LManIII, LManV, LManVI
GO:0005996	monosaccharide metabolic process	GO_BP	0.0003632	0.0000011	6.17	5	Gnmt, LManIII, LManV, LManVI, smp-30
GO:0005996	monosaccharide metabolic process	GO_BP	0.0003632	0.0000037	6.17	5	Gnmt, LManIII, LManV, LManVI, smp-30
GO:0004559	alpha-mannosidase activity	GO_MF	0.0005527	0.0000011	21.43	3	LManIII, LManV, LManVI
GO:0004559	alpha-mannosidase activity	GO_MF	0.0005527	0.0000037	21.43	3	LManIII, LManV, LManVI
GO:0015923	mannosidase activity	GO_MF	0.0006705	0.0000011	20.00	3	LManIII, LManV, LManVI
GO:0015923	mannosidase activity	GO_MF	0.0006705	0.0000037	20.00	3	LManIII, LManV, LManVI
R-DME:1474290	Collagen formation	REACTOME	0.0007187	0.0075793	8.70	4	CG4847, Spn75F, Spn77Bb, Spn77Bc
GO:0006805	xenobiotic metabolic process	GO_BP	0.0011273	0.0002321	16.67	3	CG17322, Cyp6t1, St3
GO:0071466	cellular response to xenobiotic stimulus	GO_BP	0.0011273	0.0002321	16.67	3	CG17322, Cyp6t1, St3
KEGG:00511	Other glycan degradation	KEGG	0.0023452	0.0000011	13.04	3	LManIII, LManV, LManVI
KEGG:00511	Other glycan degradation	KEGG	0.0023452	0.0000037	13.04	3	LManIII, LManV, LManVI
GO:0019318	hexose metabolic process	GO_BP	0.0036665	0.0000011	5.63	4	Gnmt, LManIII, LManV, LManVI
GO:0019318	hexose metabolic process	GO_BP	0.0036665	0.0000037	5.63	4	Gnmt, LManIII, LManV, LManVI
R-DME:194002	Glucocorticoid biosynthesis	REACTOME	0.0049632	0.0075793	10.00	3	Spn75F, Spn77Bb, Spn77Bc
R-DME:140837	Intrinsic Pathway of Fibrin Clot Formation	REACTOME	0.0053045	0.0075793	9.68	3	Spn75F, Spn77Bb, Spn77Bc
R-DME:140875	Common Pathway of Fibrin Clot Formation	REACTOME	0.0053045	0.0075793	9.68	3	Spn75F, Spn77Bb, Spn77Bc
R-DME:140877	Formation of Fibrin Clot (Clotting Cascade)	REACTOME	0.0053045	0.0075793	9.68	3	Spn75F, Spn77Bb, Spn77Bc
R-DME:3000178	ECM proteoglycans	REACTOME	0.0061930	0.0075793	9.09	3	Spn75F, Spn77Bb, Spn77Bc
R-DME:375276	Peptide ligand-binding receptors	REACTOME	0.0063081	0.0075793	8.82	3	Spn75F, Spn77Bb, Spn77Bc
R-DME:1474244	Extracellular matrix organization	REACTOME	0.0064470	0.0075793	4.71	4	CG4847, Spn75F, Spn77Bb, Spn77Bc
GO:0004867	serine-type endopeptidase inhibitor activity	GO_BP	0.0064470	0.0075793	4.71	4	Sfp24Ba, Spn75F, Spn77Bb, Spn77Bc
R-DME:1650814	Collagen biosynthesis and modifying enzymes	REACTOME	0.0084787	0.0075793	7.89	3	Spn75F, Spn77Bb, Spn77Bc
R-DME:5694530	Cargo concentration in the ER	REACTOME	0.0105451	0.0075793	7.14	3	Spn75F, Spn77Bb, Spn77Bc
GO:0046662	regulation of oviposition	GO_BP	0.0109753	0.0029724	22.22	2	Dup99B, Est-6
GO:0000023	maltose metabolic process	GO_BP	0.0125930	0.0000037	20.00	2	Mal-A4, Mal-B1
GO:0032450	maltose alpha-glucosidase activity	GO_BP	0.0125930	0.0000037	20.00	2	Mal-A4, Mal-B1
GO:0004558	alpha-1,4-glucosidase activity	GO_MF	0.0125930	0.0000037	20.00	2	Mal-A4, Mal-B1
KEGG:00040	Pentose and glucuronate interconversions	KEGG	0.0136176	0.0136176	4.00	2	CG17322, Sodh-1
GO:0090599	alpha-glucosidase activity	GO_MF	0.0175867	0.0000037	16.67	2	Mal-A4, Mal-B1
GO:0060180	female mating behavior	GO_BP	0.0213179	0.0029724	4.55	2	Dup99B, Est-6
R-DME:192456	Digestion of dietary lipid	REACTOME	0.0215175	0.0024768	5.36	3	CG18258, CG18284, CG5162
KEGG:00061	Fatty acid biosynthesis	KEGG	0.0219442	0.0026087	14.29	2	FASN3, bgm
GO:0046364	monosaccharide biosynthetic process	GO_BP	0.0219442	0.0000011	14.29	2	Gnmt, smp-30
R-DME:196071	Metabolism of steroid hormones	REACTOME	0.0259664	0.0075793	4.76	3	Spn75F, Spn77Bb, Spn77Bc
GO:0009311	oligosaccharide metabolic process	GO_BP	0.0266042	0.0000037	5.00	2	Mal-A4, Mal-B1
GO:0015926	glucosidase activity	GO_MF	0.0273663	0.0000037	12.50	2	Mal-A4, Mal-B1
GO:0004806	triglyceride lipase activity	GO_MF	0.0280498	0.0024768	4.55	3	CG18258, CG18284, CG5162
R-DME:373076	Class A/1 (Rhodopsin-like receptors)	REACTOME	0.0280498	0.0075793	4.55	3	Spn75F, Spn77Bb, Spn77Bc
GO:0018991	oviposition	GO_BP	0.0292499	0.0029724	11.11	2	Dup99B, Est-6
R-DME:204005	COPII-mediated vesicle transport	REACTOME	0.0305319	0.0075793	4.23	3	Spn75F, Spn77Bb, Spn77Bc
R-DME:500792	GPCR ligand binding	REACTOME	0.0308563	0.0075793	4.11	3	Spn75F, Spn77Bb, Spn77Bc
GO:0080030	methyl indole-3-acetate esterase activity	GO_MF	0.0321150	0.0024768	5.26	2	CG5162, Est-6
GO:0080030	methyl indole-3-acetate esterase activity	GO_MF	0.0321150	0.0029724	5.26	2	CG5162, Est-6
GO:0005984	disaccharide metabolic process	GO_BP	0.0323987	0.0000037	9.52	2	Mal-A4, Mal-B1
GO:0046008	regulation of female receptivity, post-mating	GO_BP	0.0328228	0.0029724	9.09	2	Dup99B, Est-6
R-DME:189200	Cellular hexose transport	REACTOME	0.0357865	0.0065066	8.33	2	CG1208, CG6484
GO:0045924	regulation of female receptivity	GO_BP	0.0381167	0.0029724	5.41	2	Dup99B, Est-6
GO:0004467	long-chain fatty acid-CoA ligase activity	GO_BP	0.0410941	0.0026087	7.41	2	CG4830, bgm
KEGG:00052	Galactose metabolism	KEGG	0.0433653	0.0000037	5.56	2	Mal-A4, Mal-B1
R-DME:1482801	Acyl chain remodelling of PS	REACTOME	0.0452553	0.0024768	5.88	2	CG18258, CG5162
GO:0016878	acid-thiol ligase activity	GO_MF	0.0452553	0.0026087	5.88	2	CG4830, bgm
R-DME:1482801	Acyl chain remodelling of PS	REACTOME	0.0452553	0.0029724	5.88	2	CG18258, CG5162
GO:0016405	CoA-ligase activity	GO_MF	0.0455262	0.0026087	6.67	2	CG4830, bgm
GO:0015645	fatty acid ligase activity	GO_MF	0.0455262	0.0026087	6.67	2	CG4830, bgm
GO:0001676	long-chain fatty acid metabolic process	GO_BP	0.0459347	0.0026087	6.25	2	CG4830, bgm
KEGG:00500	Starch and sucrose metabolism	KEGG	0.0459347	0.0000037	6.25	2	Mal-A4, Mal-B1

This figure is related to Figure 7 (right)

ClueGOResultTable_TDOWN_PDOWN_1.6_cur <- read.csv("Analysis/ClueGOResultTable_TDOWN_PDOWN_det_results_curated.csv",  header = TRUE, sep = ",")

ClueGOResultTable_TDOWN_PDOWN_1.6_cur <- as.data.frame(ClueGOResultTable_TDOWN_PDOWN_1.6_cur)
ClueGOResultTable_TDOWN_PDOWN_1.6_cur  <- ClueGOResultTable_TDOWN_PDOWN_1.6_cur %>% arrange((Term_Pvalue_Corrected_with_Bonferroni_step_down))
ClueGOResultTable_TDOWN_PDOWN_1.6_cur <- ClueGOResultTable_TDOWN_PDOWN_1.6_cur %>% mutate(GOTerm = fct_reorder(GOTerm, desc(Term_Pvalue_Corrected_with_Bonferroni_step_down))) # lock in factor level order


str(ClueGOResultTable_TDOWN_PDOWN_1.6_cur)

## 'data.frame':    15 obs. of  11 variables:
##  $ GOID                                            : Factor w/ 15 levels "GO:0004553","GO:0004806",..: 1 15 4 10 5 13 9 3 14 7 ...
##  $ GOTerm                                          : Factor w/ 15 levels "Acyl chain remodelling of PS",..: 15 14 13 12 11 10 8 9 7 6 ...
##  $ OS_short                                        : Factor w/ 4 levels "GO_BP","GO_MF",..: 2 4 1 4 1 4 4 1 4 3 ...
##  $ Ontology_Source                                 : Factor w/ 4 levels "GO_BiologicalProcess-EBI-UniProt-GOA-ACAP-ARAP_15.01.2021_00h00",..: 2 4 1 4 1 4 4 1 4 3 ...
##  $ Term_PValue                                     : num  9.00e-07 1.50e-06 9.60e-06 2.05e-05 3.32e-05 ...
##  $ Term_Pvalue_Corrected_with_Bonferroni_step_down : num  3.68e-05 5.99e-05 3.63e-04 7.19e-04 1.13e-03 ...
##  $ Group_PValue                                    : num  1.00e-07 1.00e-07 1.00e-07 2.53e-03 3.32e-05 ...
##  $ Group_PValue_Corrected_with_Bonferroni_step_down: num  1.10e-06 1.10e-06 1.10e-06 7.58e-03 2.32e-04 ...
##  $ X._Associated_Genes                             : num  6.45 42.86 6.17 8.7 16.67 ...
##  $ No_Genes                                        : int  6 3 5 4 3 3 4 4 3 2 ...
##  $ Associated_Genes_Found                          : Factor w/ 13 levels "CG1208, CG6484",..: 11 10 9 6 2 13 6 12 13 3 ...

ClueGOResultTable_TDOWN_PDOWN_1.6_cur_plot <- ggplot( ClueGOResultTable_TDOWN_PDOWN_1.6_cur, aes(x = -log10(Term_Pvalue_Corrected_with_Bonferroni_step_down), y = GOTerm, fill= OS_short)) + geom_bar(stat="identity", width=0.7 ) + scale_fill_brewer(palette="RdBu") +  theme_bw() + ylab(NULL) + xlab("-log10(term adjusted p value)") + theme(legend.position="right", text = element_text(size=15)) + geom_text(aes(label=No_Genes ), size=3, nudge_x = .7, color = "black" )  + scale_x_continuous(expand = c(0, 0), limits = c(0, 8)) + guides(fill=guide_legend(title="Ontology"))

ClueGOResultTable_TDOWN_PDOWN_1.6_cur_plot

ggsave("1.6_figure_output/ClueGOResultTable_TDOWN_PDOWN_1.6_cur_plot.pdf", scale = 1, dpi = 320, width = 9, limitsize = TRUE)

## Saving 9 x 5 in image

uORF Analysis

**uORF data taken from Supplementary Table 1 “Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development, Zhang et al., 2018” (https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2003903)**

This analysis is related to Figure 5.

# Load datasets  

library(readr)
ORF <- read_csv("1.6_data/ORF.csv") # Table S1 from the Zhang et al., 2018 paper 

## Parsed with column specification:
## cols(
##   Chromosome = col_character(),
##   Start = col_double(),
##   End = col_double(),
##   Strand = col_character(),
##   Gene_ID = col_character(),
##   Isoform = col_character()
## )

Group1 <- read_csv("1.6_data/FlyBase_ID_Group1.csv")  # Group 1 genes 

## Parsed with column specification:
## cols(
##   Isoform = col_character(),
##   Gene_ID = col_character(),
##   symbol = col_character()
## )

Group2 <- read_csv("1.6_data/FlyBase_IDs_Group2.csv") # Group 2 genes 

## Parsed with column specification:
## cols(
##   Isoform = col_character(),
##   Gene_ID = col_character(),
##   Symbol = col_character()
## )

# Inner join 

# Group 1 genes 
ORF_G1 <- inner_join(ORF, Group1, by = "Isoform")
ORF_G1unq <- ORF_G1 %>% select(symbol) %>% unique() # 8/27 targets 29.6%
write.csv(ORF_G1, "1.6_data_output/ORF_G1_merge_group1.csv") # Supplemntary figure 17

# Group 2 genes 
ORF_G2 <- inner_join(ORF, Group2, by = "Isoform")
ORF_G2unq <- ORF_G2 %>% select(Symbol) %>% unique() # 40/102 targets 39.2%
write.csv(ORF_G2, "1.6_data_output/ORF_G2_merge_group2.csv") # Supplemntary figure 18


#Total targets inner join - only matched transcripts and proteins 

Total_ORF <- read_csv("1.6_data/dPERK_inner_join_FC1.6_ORF.csv") # changed column name Transcript ID to Isoform for the merging in excel 

## Parsed with column specification:
## cols(
##   Isoform = col_character(),
##   Gene.name = col_character(),
##   Protein.ID = col_character(),
##   trans_FC = col_double(),
##   trans_FDR = col_double(),
##   prot_FC = col_double(),
##   prot_FDR = col_double(),
##   trans_reg = col_double(),
##   prot_reg = col_double()
## )

Total_ORFunq <- Total_ORF %>% select(Gene.name) %>% unique() # 5,586 genes 

# Merge datasets 
ORF_total <- inner_join(ORF, Total_ORF, by = "Isoform") # 9,059 transcripts
ORF_totalunq <- ORF_total %>% select(Gene.name) %>% unique() # 2,425 genes with uORF
 
write.csv(ORF_total, "1.6_data_output/ORFtotala_merge_dPERK_inner_join.csv") # Supplemntary figure 16

Percentage of uORFs

group_names <- c("Total", "Group 1", "Group 2")
percentages_uORF <- c((2425/5586*100), (7/26*100), (40/102*100))

Fig5a <- data.frame(group_names, percentages_uORF)


Fig5a_plot <-ggplot(data= Fig5a , aes(x= group_names, y= percentages_uORF )) +
  geom_bar(stat="identity") + scale_y_continuous(limits = c(0,50), breaks = seq(0, 50, by = 25))
Fig5a_plot

ggsave("1.6_figure_output/Fig5a.pdf", scale = 1, dpi = 320, width = 9, limitsize = TRUE)

## Saving 9 x 5 in image

Group 1 uORFs

first_column <- c("CG43402", "CG31808", "Dgp-1", "Hsp22", "CG2017", "Ire1", "BomBc3" )
second_column <- c(1, 3, 6, 15, 2, 4, 1)

Group1_nouORF <- data.frame(first_column, second_column)
Group1_nouORF 

##   first_column second_column
## 1      CG43402             1
## 2      CG31808             3
## 3        Dgp-1             6
## 4        Hsp22            15
## 5       CG2017             2
## 6         Ire1             4
## 7       BomBc3             1

Group1_nouORF_plot <-ggplot(data=Group1_nouORF , aes(x=first_column, y=second_column)) +
  geom_bar(stat="identity") + scale_y_continuous(breaks = seq(0, 15, by = 1))
Group1_nouORF_plot

ggsave("1.6_figure_output/Group1_nouORF_plot.pdf", scale = 1, dpi = 320, width = 9, limitsize = TRUE)

## Saving 9 x 5 in image

Monte carlo

# Groups    | uORFpresent   | uORF absent   | Sum
# -------------------------------------------
# Total   | 2,425         | 3161          | 5,586
# Group 1 | 7             | 19          | 26
# Group 2   | 40            | 62            | 102

orf_pior = 2425/5586


# Group 1
group1_size = 26
group1_test = 7
# generate int values of size 27 based on orf prior

#variance: mean - 3sd = 0
set.seed(3)
sd_g1 = orf_pior*group1_size/(3)
mc_dt = round(rnorm(1000, mean=orf_pior*group1_size, sd=sd_g1))

t.test(mc_dt, mu = group1_test, alternative = "two.sided")

## 
##  One Sample t-test
## 
## data:  mc_dt
## t = 36.217, df = 999, p-value < 2.2e-16
## alternative hypothesis: true mean is not equal to 7
## 95 percent confidence interval:
##  11.06607 11.53193
## sample estimates:
## mean of x 
##    11.299

p_val_list1 = c()
for (i in 1:1000){
  sd_g1 = orf_pior*group1_size/(3)
  mc_dt_g1 = round(rnorm(100, mean=orf_pior*group1_size, sd=sd_g1))
  t = t.test(mc_dt_g1, mu = group1_test, alternative = "two.sided") 
  p_val_list1 = c(p_val_list1, t$p.value)
}
adj_p_val1 = sum(p_val_list1 >= 0.05, na.rm = TRUE)/1000
adj_p_val1

## [1] 0

#negative control:
t.test(mc_dt, mu = orf_pior*group1_size, alternative = "two.sided") # not sig

## 
##  One Sample t-test
## 
## data:  mc_dt
## t = 0.099862, df = 999, p-value = 0.9205
## alternative hypothesis: true mean is not equal to 11.28715
## 95 percent confidence interval:
##  11.06607 11.53193
## sample estimates:
## mean of x 
##    11.299

# Group 2
group2_size = 102
group2_test = 40
# generate int values of size 27 based on orf prior

p_val_list2 = c()

for (i in 1:1000){
  sd_g2 = orf_pior*group2_size/(3)
  mc_dt_g2 = round(rnorm(100, mean=orf_pior*group2_size, sd=sd_g2))
  t = t.test(mc_dt_g2, mu = group2_test, alternative = "two.sided") 
  p_val_list2 = c(p_val_list2, t$p.value)
}

adj_p_val2 = sum(p_val_list2 >= 0.05, na.rm = TRUE)/1000
adj_p_val2

## [1] 0.188

#sqrt(orf_pior*group2_size)
#negative control:
t.test(mc_dt_g2, mu = orf_pior*group2_size, alternative = "two.sided") # not sig

## 
##  One Sample t-test
## 
## data:  mc_dt_g2
## t = -1.0456, df = 99, p-value = 0.2983
## alternative hypothesis: true mean is not equal to 44.28034
## 95 percent confidence interval:
##  39.44016 45.77984
## sample estimates:
## mean of x 
##     42.61

Comparison of number of uORFs per genes

#Total merged minus group 1

g1 = ORF_G1
g1 <- g1 %>% dplyr::rename(Gene_ID = Gene_ID.x) #rename for antijoin 
                
ORF_total_minusg1_antijoin <- anti_join(ORF_total, g1, by = "Gene_ID")   #return all rows from x where there are not matching values in y, keeping just columns from x
ORF_total_minusg1 <- ORF_total_minusg1_antijoin
ORF_total_minusg1 <- data.frame(Gene = ORF_total_minusg1$Gene_ID) #dataframe with just genes 
 
ORF_total_minusg1 = ORF_total_minusg1 %>% 
  group_by(Gene) %>%
  summarise(count = length(Gene))

## `summarise()` ungrouping output (override with `.groups` argument)

# group 1

g1_grouped = g1
g1_grouped <- g1_grouped %>% filter(!symbol == "PEK")
g1_grouped = g1_grouped %>% 
  group_by(symbol) %>%
  summarise(count = length(symbol)) 

## `summarise()` ungrouping output (override with `.groups` argument)

#group 2

g2 = ORF_G2
g2_grouped = g2
g2_grouped = g2_grouped %>% 
  group_by(Symbol) %>%
  summarise(count = length(Symbol))

## `summarise()` ungrouping output (override with `.groups` argument)

#compare them 

wilcox.test(g2_grouped$count,g1_grouped$count, exact = FALSE)

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  g2_grouped$count and g1_grouped$count
## W = 129, p-value = 0.7484
## alternative hypothesis: true location shift is not equal to 0

# does not have a different number of uORFs

wilcox.test(ORF_total_minusg1$count,g1_grouped$count)

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  ORF_total_minusg1$count and g1_grouped$count
## W = 7278.5, p-value = 0.51
## alternative hypothesis: true location shift is not equal to 0

# does not have a different number of uORFs

Comparison of lenght of uORFs per genes

#check length

# group 1
g1_length = g1
g1_length = g1_length %>% filter(!symbol == "PEK")
g1_length$l = g1_length$End-g1_length$Start
g1_length$l

##  [1]   15   27  129   69   21 1127   15   63   12   18  470  186  168   21  206
## [16]   77   57   57   21   87   87   57   12   84   84   18    6   27   18    6
## [31]   27   48

hist(g1_length$l)

summary(g1_length$l)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    6.00   18.00   52.50  103.75   84.75 1127.00

# Total merged minus group 1
ORF_total_minusg1_length = ORF_total_minusg1_antijoin
ORF_total_minusg1_length$l = ORF_total_minusg1_length$End - ORF_total_minusg1_length$Start
hist(ORF_total_minusg1_length$l)

summary(ORF_total_minusg1_length$l)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##     3.0    18.0    36.0   329.9    84.0 73938.0

# group 2
g2_length = g2
g2_length$l = g2_length$End-g2_length$Start
hist(g2_length$l)

summary(g2_length$l)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##       6      18      42     111      78    4919

wilcox.test(g2_length$l,g1_length$l)

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  g2_length$l and g1_length$l
## W = 3031.5, p-value = 0.7636
## alternative hypothesis: true location shift is not equal to 0

# does not have a different lenghts of uORFs

wilcox.test(ORF_total_minusg1_length$l,g1_length$l)

## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  ORF_total_minusg1_length$l and g1_length$l
## W = 138150, p-value = 0.6727
## alternative hypothesis: true location shift is not equal to 0

# does not have a different lenghts of uORFs