Example gene set analysis: The case of SARS-CoV2 infection
Mark Ziemann & Kaumadi Wijesooriya
2022-01-25
Source: https://github.com/markziemann/combined_enrichment
Intro
Here we are performing an analysis of some gene expression data to demonstrate the difference between ORA and FCS methods and to highlight the differences caused by improper background gene set use.
The dataset being used is SRP253951 and we are comparing A549 cells with and without infection with SARS-CoV-2.
Data are obtained from http://dee2.io/
suppressPackageStartupMessages({
library("getDEE2")
library("DESeq2")
library("clusterProfiler")
library("mitch")
library("kableExtra")
library("eulerr")
})Get expression data
I’m using some RNA-seq data looking at the difference in transcriptome caused by SARS-CoV-2 infection.
name="SRP253951"
mdat<-getDEE2Metadata("hsapiens")
samplesheet <- mdat[grep("SRP253951",mdat$SRP_accession),]
samplesheet <- mdat[which(mdat$SRX_accession %in% c("SRX8089264","SRX8089265","SRX8089266","SRX8089267","SRX8089268","SRX8089269")),]
samplesheet$trt <- factor(c(0,0,0,1,1,1))
s1 <- samplesheet
s1 %>% kbl(caption = "sample sheet") %>% kable_paper("hover", full_width = F)| SRR_accession | QC_summary | SRX_accession | SRS_accession | SRP_accession | Sample_name | GEO_series | Library_name | trt | |
|---|---|---|---|---|---|---|---|---|---|
| 229503 | SRR11517674 | PASS | SRX8089264 | SRS6456133 | SRP253951 | GSM4462336 | GSE147507 | 0 | |
| 229504 | SRR11517675 | PASS | SRX8089265 | SRS6456134 | SRP253951 | GSM4462337 | GSE147507 | 0 | |
| 229505 | SRR11517676 | PASS | SRX8089266 | SRS6456135 | SRP253951 | GSM4462338 | GSE147507 | 0 | |
| 229506 | SRR11517677 | PASS | SRX8089267 | SRS6456136 | SRP253951 | GSM4462339 | GSE147507 | 1 | |
| 229507 | SRR11517678 | PASS | SRX8089268 | SRS6456137 | SRP253951 | GSM4462340 | GSE147507 | 1 | |
| 229508 | SRR11517679 | PASS | SRX8089269 | SRS6456139 | SRP253951 | GSM4462341 | GSE147507 | 1 |
w<-getDEE2("hsapiens",samplesheet$SRR_accession,metadata=mdat,legacy = TRUE)## For more information about DEE2 QC metrics, visit
## https://github.com/markziemann/dee2/blob/master/qc/qc_metrics.mdx<-Tx2Gene(w)
x <- x$Tx2Gene
# save the genetable for later
gt<-w$GeneInfo[,1,drop=FALSE]
gt$accession<-rownames(gt)
# counts
x1<-x[,which(colnames(x) %in% samplesheet$SRR_accession)]Here show the number of genes in the annotation set, and those detected above the detection threshold.
# filter out lowly expressed genes
x1<-x1[which(rowSums(x1)/ncol(x1)>=(10)),]
nrow(x)## [1] 39297nrow(x1)## [1] 15182Now multidimensional scaling (MDS) plot to show the correlation between the datasets. If the control and case datasets are clustered separately, then it is likely that there will be many differentially expressed genes with FDR<0.05.
plot(cmdscale(dist(t(x1))), xlab="Coordinate 1", ylab="Coordinate 2", pch=19, col=s1$trt, main="MDS")
Differential expression
Now run DESeq2 for control vs case.
y <- DESeqDataSetFromMatrix(countData = round(x1), colData = s1, design = ~ trt)## converting counts to integer modey <- DESeq(y)## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testingde <- results(y)
de<-as.data.frame(de[order(de$pvalue),])
rownames(de)<-sapply(strsplit(rownames(de),"\\."),"[[",1)
head(de) %>% kbl() %>% kable_paper("hover", full_width = F)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
|---|---|---|---|---|---|---|
| ENSG00000113739 | 3523.734 | 4.004593 | 0.1012568 | 39.54888 | 0 | 0 |
| ENSG00000176153 | 8851.309 | -2.785312 | 0.0820808 | -33.93378 | 0 | 0 |
| ENSG00000058085 | 5767.111 | 3.699041 | 0.1148334 | 32.21223 | 0 | 0 |
| ENSG00000169710 | 6917.854 | -2.259158 | 0.0703230 | -32.12547 | 0 | 0 |
| ENSG00000170421 | 41561.919 | -2.233482 | 0.0742019 | -30.10007 | 0 | 0 |
| ENSG00000100297 | 2476.082 | -2.364383 | 0.0802583 | -29.45965 | 0 | 0 |
Now let’s have a look at some of the charts showing differential expression. In particular, an MA plot and volcano plot.
maplot <- function(de,contrast_name) {
sig <-subset(de, padj < 0.05 )
up <-rownames(subset(de, padj < 0.05 & log2FoldChange > 0))
dn <-rownames(subset(de, padj < 0.05 & log2FoldChange < 0))
GENESUP <- length(up)
GENESDN <- length(dn)
DET=nrow(de)
SUBHEADER = paste(GENESUP, "up, ", GENESDN, "down", DET, "detected")
ns <-subset(de, padj > 0.05 )
plot(log2(de$baseMean),de$log2FoldChange,
xlab="log2 basemean", ylab="log2 foldchange",
pch=19, cex=0.5, col="dark gray",
main=contrast_name, cex.main=0.7)
points(log2(sig$baseMean),sig$log2FoldChange,
pch=19, cex=0.5, col="red")
mtext(SUBHEADER,cex = 0.7)
}
make_volcano <- function(de,name) {
sig <- subset(de,padj<0.05)
N_SIG=nrow(sig)
N_UP=nrow(subset(sig,log2FoldChange>0))
N_DN=nrow(subset(sig,log2FoldChange<0))
DET=nrow(de)
HEADER=paste(N_SIG,"@5%FDR,", N_UP, "up", N_DN, "dn", DET, "detected")
plot(de$log2FoldChange,-log10(de$padj),cex=0.5,pch=19,col="darkgray",
main=name, xlab="log2 FC", ylab="-log10 pval", xlim=c(-6,6))
mtext(HEADER)
grid()
points(sig$log2FoldChange,-log10(sig$padj),cex=0.5,pch=19,col="red")
}
maplot(de,name)
make_volcano(de,name)
Gene sets from Reactome
In order to perform gene set analysis, we need some gene sets.
if (! file.exists("ReactomePathways.gmt")) {
download.file("https://reactome.org/download/current/ReactomePathways.gmt.zip",
destfile="ReactomePathways.gmt.zip")
unzip("ReactomePathways.gmt.zip")
}
genesets<-gmt_import("ReactomePathways.gmt")FCS with Mitch
Mitch uses rank-ANOVA statistics for enrichment detection.
Here I’m using the standard approach
m <- mitch_import(de,DEtype = "DEseq2", geneTable = gt)## The input is a single dataframe; one contrast only. Converting
## it to a list for you.## Note: Mean no. genes in input = 15182## Note: no. genes in output = 14186## Note: estimated proportion of input genes in output = 0.934msep <- mitch_calc(m,genesets = genesets)## Note: When prioritising by significance (ie: small
## p-values), large effect sizes might be missed.ms_up <- subset(msep$enrichment_result,p.adjustANOVA<0.05 & s.dist > 0)[,1]
ms_dn <- subset(msep$enrichment_result,p.adjustANOVA<0.05 & s.dist < 0)[,1]
message(paste("Number of up-regulated pathways:",length(ms_up) ))## Number of up-regulated pathways: 98message(paste("Number of down-regulated pathways:",length(ms_dn) ))## Number of down-regulated pathways: 322head(msep$enrichment_result,10) #%>% kbl() %>% kable_paper("hover", full_width = F)## set setSize pANOVA
## 146 Cell Cycle 597 7.956293e-38
## 148 Cell Cycle, Mitotic 481 1.890060e-33
## 234 DNA Replication 128 1.071526e-24
## 1174 Synthesis of DNA 117 1.260311e-22
## 827 Processing of Capped Intron-Containing Pre-mRNA 236 1.122694e-20
## 147 Cell Cycle Checkpoints 250 7.131152e-20
## 1346 mRNA Splicing - Major Pathway 178 2.816119e-19
## 1345 mRNA Splicing 186 3.042727e-19
## 595 M Phase 342 6.481834e-19
## 409 G2/M Checkpoints 131 1.291529e-18
## s.dist p.adjustANOVA
## 146 -0.3095063 1.090808e-34
## 148 -0.3219944 1.295636e-30
## 234 -0.5250080 4.896875e-22
## 1174 -0.5238061 4.319716e-20
## 827 -0.3528510 3.078427e-18
## 147 -0.3357336 1.629468e-17
## 1346 -0.3903556 5.214473e-17
## 1345 -0.3816160 5.214473e-17
## 595 -0.2803765 9.873994e-17
## 409 -0.4457228 1.770686e-16#mitch_report(msep,outfile="mitch_separate.html",overwrite=TRUE)Here I’m using the combined approach.
mcom <- mitch_calc(abs(m),genesets = genesets)## Note: When prioritising by significance (ie: small
## p-values), large effect sizes might be missed.mc_up <- subset(mcom$enrichment_result,p.adjustANOVA<0.05 & s.dist > 0)[,1]
mc_dn <- subset(mcom$enrichment_result,p.adjustANOVA<0.05 & s.dist < 0)[,1]
message(paste("Number of up-regulated pathways:",length(mc_up) ))## Number of up-regulated pathways: 352message(paste("Number of down-regulated pathways:",length(mc_dn) ))## Number of down-regulated pathways: 3head(mcom$enrichment_result,10) #%>% kbl() %>% kable_paper("hover", full_width = F)## set setSize pANOVA s.dist p.adjustANOVA
## 148 Cell Cycle, Mitotic 481 2.390793e-24 0.2722246 3.277777e-21
## 146 Cell Cycle 597 7.302058e-24 0.2427684 5.005561e-21
## 508 Immune System 1391 1.996201e-15 0.1293148 7.300462e-13
## 1068 Signal Transduction 1861 2.129967e-15 0.1137957 7.300462e-13
## 236 DNA strand elongation 32 8.476618e-14 0.7618385 2.324289e-11
## 1174 Synthesis of DNA 117 7.429390e-13 0.3840492 1.697616e-10
## 234 DNA Replication 128 1.951557e-12 0.3604998 3.822263e-10
## 276 Disease 1249 2.993960e-12 0.1192802 5.130898e-10
## 595 M Phase 342 6.862328e-12 0.2166501 1.045361e-09
## 162 Cellular responses to stimuli 634 1.477304e-11 0.1582427 1.844476e-09#mitch_report(mcom,outfile="mitch_combined.html",overwrite=TRUE)Let’s look at the significant ones based on the combined analysis. There weren’t many gene sets classe d as significant. Let’s see how many have a direction agnostic enrichment score which is larger in magnitude than the direction informed enrichment score. There are only 11 such sets which would benefit from such combined analysis.
Euler diagram of the significant pathways found with each approach.
l0 <- list("sep up"=ms_up,"sep dn"=ms_dn,"comb up"=mc_up,"comb dn"=mc_dn)
par(cex.main=0.5)
plot(euler(l0),quantities = TRUE, edges = "gray", main="FCS: combined vs separated")
length(ms_up)## [1] 98length(ms_dn)## [1] 322length(ms_up)+length(ms_dn)## [1] 420length(mc_up)## [1] 352length(mc_dn)## [1] 3length(mc_up)+length(mc_dn)## [1] 355( length(ms_up)+length(ms_dn) ) / ( length(mc_up)+length(mc_dn) )## [1] 1.183099List gene sets which are specific to each approach.
ms <- c(ms_up,ms_dn)
# in sep but not comb
setdiff(ms,mc_up)## [1] "Eukaryotic Translation Elongation"
## [2] "Peptide chain elongation"
## [3] "Viral mRNA Translation"
## [4] "Formation of a pool of free 40S subunits"
## [5] "Selenocysteine synthesis"
## [6] "Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)"
## [7] "Eukaryotic Translation Termination"
## [8] "SRP-dependent cotranslational protein targeting to membrane"
## [9] "Selenoamino acid metabolism"
## [10] "Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)"
## [11] "Nonsense-Mediated Decay (NMD)"
## [12] "Assembly of collagen fibrils and other multimeric structures"
## [13] "FOXO-mediated transcription of cell cycle genes"
## [14] "Netrin-1 signaling"
## [15] "Formation of the ternary complex, and subsequently, the 43S complex"
## [16] "Signaling by FLT3 ITD and TKD mutants"
## [17] "BMAL1:CLOCK,NPAS2 activates circadian gene expression"
## [18] "Chemokine receptors bind chemokines"
## [19] "Ribosomal scanning and start codon recognition"
## [20] "Insulin processing"
## [21] "Amino acid transport across the plasma membrane"
## [22] "RAB GEFs exchange GTP for GDP on RABs"
## [23] "Interferon gamma signaling"
## [24] "Signal transduction by L1"
## [25] "Signaling by BMP"
## [26] "Collagen chain trimerization"
## [27] "Cell junction organization"
## [28] "Negative regulators of DDX58/IFIH1 signaling"
## [29] "Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)"
## [30] "Post-translational protein phosphorylation"
## [31] "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell"
## [32] "DCC mediated attractive signaling"
## [33] "GAB1 signalosome"
## [34] "Nicotinate metabolism"
## [35] "Integrin cell surface interactions"
## [36] "Synthesis of PIPs at the plasma membrane"
## [37] "Circadian Clock"
## [38] "Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer"
## [39] "Peptide ligand-binding receptors"
## [40] "Glutamate Neurotransmitter Release Cycle"
## [41] "Antigen activates B Cell Receptor (BCR) leading to generation of second messengers"
## [42] "Downregulation of SMAD2/3:SMAD4 transcriptional activity"
## [43] "VEGFR2 mediated cell proliferation"
## [44] "Signaling by Erythropoietin"
## [45] "ECM proteoglycans"
## [46] "Collagen biosynthesis and modifying enzymes"
## [47] "The citric acid (TCA) cycle and respiratory electron transport"
## [48] "Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins."
## [49] "Respiratory electron transport"
## [50] "Complex I biogenesis"
## [51] "FBXL7 down-regulates AURKA during mitotic entry and in early mitosis"
## [52] "Nucleotide Excision Repair"
## [53] "SCF-beta-TrCP mediated degradation of Emi1"
## [54] "Cross-presentation of soluble exogenous antigens (endosomes)"
## [55] "Asymmetric localization of PCP proteins"
## [56] "Ubiquitin Mediated Degradation of Phosphorylated Cdc25A"
## [57] "p53-Independent DNA Damage Response"
## [58] "p53-Independent G1/S DNA damage checkpoint"
## [59] "Negative regulation of NOTCH4 signaling"
## [60] "Transport of Mature Transcript to Cytoplasm"
## [61] "Regulation of ornithine decarboxylase (ODC)"
## [62] "Vif-mediated degradation of APOBEC3G"
## [63] "Vpu mediated degradation of CD4"
## [64] "G2/M DNA damage checkpoint"
## [65] "Ubiquitin-dependent degradation of Cyclin D"
## [66] "Regulation of activated PAK-2p34 by proteasome mediated degradation"
## [67] "Degradation of DVL"
## [68] "tRNA processing"
## [69] "Degradation of GLI2 by the proteasome"
## [70] "Global Genome Nucleotide Excision Repair (GG-NER)"
## [71] "UCH proteinases"
## [72] "Degradation of GLI1 by the proteasome"
## [73] "Autodegradation of the E3 ubiquitin ligase COP1"
## [74] "GLI3 is processed to GLI3R by the proteasome"
## [75] "SUMOylation of DNA replication proteins"
## [76] "PCP/CE pathway"
## [77] "Transcriptional regulation by small RNAs"
## [78] "Regulation of Apoptosis"
## [79] "Transport of Mature mRNA derived from an Intron-Containing Transcript"
## [80] "Hh mutants are degraded by ERAD"
## [81] "HSF1-dependent transactivation"
## [82] "Regulation of HMOX1 expression and activity"
## [83] "Hh mutants abrogate ligand secretion"
## [84] "Protein localization"
## [85] "Metabolism of polyamines"
## [86] "ROS sensing by NFE2L2"
## [87] "mRNA 3'-end processing"
## [88] "Regulation of RUNX3 expression and activity"
## [89] "Viral Messenger RNA Synthesis"
## [90] "NIK-->noncanonical NF-kB signaling"
## [91] "Cytoprotection by HMOX1"
## [92] "Attenuation phase"
## [93] "Dectin-1 mediated noncanonical NF-kB signaling"
## [94] "tRNA processing in the nucleus"
## [95] "Hedgehog ligand biogenesis"
## [96] "Mitochondrial protein import"
## [97] "Defective CFTR causes cystic fibrosis"
## [98] "Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha"
## [99] "Deposition of new CENPA-containing nucleosomes at the centromere"
## [100] "Nucleosome assembly"
## [101] "Regulation of RUNX2 expression and activity"
## [102] "ER-Phagosome pathway"
## [103] "RUNX1 regulates transcription of genes involved in differentiation of HSCs"
## [104] "Metabolism of steroids"
## [105] "Glucose metabolism"
## [106] "Stabilization of p53"
## [107] "Defective pyroptosis"
## [108] "Metabolism of non-coding RNA"
## [109] "snRNP Assembly"
## [110] "TCF dependent signaling in response to WNT"
## [111] "Transport of Mature mRNAs Derived from Intronless Transcripts"
## [112] "Polo-like kinase mediated events"
## [113] "Activation of NF-kappaB in B cells"
## [114] "SUMO E3 ligases SUMOylate target proteins"
## [115] "Metabolism of porphyrins"
## [116] "ABC-family proteins mediated transport"
## [117] "E2F mediated regulation of DNA replication"
## [118] "ABC transporter disorders"
## [119] "Diseases of DNA repair"
## [120] "Transport of Mature mRNA Derived from an Intronless Transcript"
## [121] "Formation of the Early Elongation Complex"
## [122] "Formation of the HIV-1 Early Elongation Complex"
## [123] "Heme biosynthesis"
## [124] "Gene Silencing by RNA"
## [125] "Degradation of beta-catenin by the destruction complex"
## [126] "SUMOylation"
## [127] "Fanconi Anemia Pathway"
## [128] "Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol"
## [129] "Hedgehog 'on' state"
## [130] "TP53 Regulates Transcription of DNA Repair Genes"
## [131] "Formation of RNA Pol II elongation complex"
## [132] "RNA Polymerase II Transcription Elongation"
## [133] "Antigen processing-Cross presentation"
## [134] "Rev-mediated nuclear export of HIV RNA"
## [135] "Epigenetic regulation of gene expression"
## [136] "Regulation of TP53 Activity through Acetylation"
## [137] "Cytosolic iron-sulfur cluster assembly"
## [138] "Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)"
## [139] "Cellular response to hypoxia"
## [140] "Formation of HIV-1 elongation complex containing HIV-1 Tat"
## [141] "HIV Transcription Elongation"
## [142] "Tat-mediated elongation of the HIV-1 transcript"
## [143] "Folding of actin by CCT/TriC"
## [144] "Glycolysis"
## [145] "Association of TriC/CCT with target proteins during biosynthesis"
## [146] "ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression"
## [147] "Regulation of RAS by GAPs"
## [148] "Transport of the SLBP Dependant Mature mRNA"
## [149] "Interactions of Rev with host cellular proteins"
## [150] "TNFR2 non-canonical NF-kB pathway"
## [151] "Export of Viral Ribonucleoproteins from Nucleus"
## [152] "Hedgehog 'off' state"
## [153] "TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest"
## [154] "Glyoxylate metabolism and glycine degradation"
## [155] "Downstream signaling events of B Cell Receptor (BCR)"
## [156] "Pyruvate metabolism and Citric Acid (TCA) cycle"
## [157] "Biological oxidations"
## [158] "Activation of gene expression by SREBF (SREBP)"
## [159] "Inhibition of DNA recombination at telomere"
## [160] "Transport of the SLBP independent Mature mRNA"
## [161] "Regulation of cholesterol biosynthesis by SREBP (SREBF)"
## [162] "Formation of HIV elongation complex in the absence of HIV Tat"
## [163] "HIV Life Cycle"
## [164] "PIWI-interacting RNA (piRNA) biogenesis"
## [165] "Gluconeogenesis"
## [166] "PRC2 methylates histones and DNA"
## [167] "RMTs methylate histone arginines"
## [168] "NEP/NS2 Interacts with the Cellular Export Machinery"
## [169] "Inhibition of replication initiation of damaged DNA by RB1/E2F1"
## [170] "Metabolism of carbohydrates"
## [171] "Lysosome Vesicle Biogenesis"
## [172] "TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest"
## [173] "Defective HDR through Homologous Recombination (HRR) due to BRCA1 loss-of-function"
## [174] "Defective HDR through Homologous Recombination (HRR) due to PALB2 loss of function"
## [175] "Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function"
## [176] "Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function"
## [177] "Diseases of DNA Double-Strand Break Repair"
## [178] "FGFR2 alternative splicing"
## [179] "FGFR2 mutant receptor activation"
## [180] "Transport of Ribonucleoproteins into the Host Nucleus"
## [181] "Nuclear import of Rev protein"
## [182] "SUMOylation of SUMOylation proteins"
## [183] "Depolymerisation of the Nuclear Lamina"
## [184] "Late Phase of HIV Life Cycle"
## [185] "SUMOylation of chromatin organization proteins"
## [186] "Nuclear Pore Complex (NPC) Disassembly"
## [187] "Base-Excision Repair, AP Site Formation"
## [188] "Downstream TCR signaling"
## [189] "MHC class II antigen presentation"
## [190] "FCERI mediated NF-kB activation"
## [191] "Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC)"
## [192] "Regulation of Glucokinase by Glucokinase Regulatory Protein"
## [193] "DNA Damage Recognition in GG-NER"
## [194] "Positive epigenetic regulation of rRNA expression"
## [195] "Synthesis of bile acids and bile salts via 24-hydroxycholesterol"
## [196] "Meiotic recombination"
## [197] "MicroRNA (miRNA) biogenesis"
## [198] "Activation of HOX genes during differentiation"
## [199] "Activation of anterior HOX genes in hindbrain development during early embryogenesis"
## [200] "Sealing of the nuclear envelope (NE) by ESCRT-III"
## [201] "Meiosis"
## [202] "Formation of TC-NER Pre-Incision Complex"
## [203] "Processing of Intronless Pre-mRNAs"
## [204] "RNA Pol II CTD phosphorylation and interaction with CE"
## [205] "RNA Pol II CTD phosphorylation and interaction with CE during HIV infection"
## [206] "Pentose phosphate pathway"
## [207] "Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters"
## [208] "Gene expression (Transcription)"
## [209] "Fatty acid metabolism"
## [210] "Interactions of Vpr with host cellular proteins"
## [211] "Signaling by Hedgehog"
## [212] "Diseases of metabolism"
## [213] "Aflatoxin activation and detoxification"
## [214] "MASTL Facilitates Mitotic Progression"
## [215] "CDC6 association with the ORC:origin complex"
## [216] "TP53 Regulates Transcription of Cell Cycle Genes"# in comb but not sep
setdiff(mc_up,ms)## [1] "Signal Transduction"
## [2] "Disease"
## [3] "Cellular responses to stimuli"
## [4] "Cellular responses to stress"
## [5] "Signaling by Rho GTPases, Miro GTPases and RHOBTB3"
## [6] "Signaling by Rho GTPases"
## [7] "PIP3 activates AKT signaling"
## [8] "Diseases of signal transduction by growth factor receptors and second messengers"
## [9] "RHO GTPase cycle"
## [10] "Neutrophil degranulation"
## [11] "PI3K/AKT Signaling in Cancer"
## [12] "Innate Immune System"
## [13] "Intracellular signaling by second messengers"
## [14] "Signaling by ERBB2"
## [15] "Developmental Biology"
## [16] "Metabolism of proteins"
## [17] "Infectious disease"
## [18] "Downregulation of ERBB2 signaling"
## [19] "MAPK family signaling cascades"
## [20] "Negative regulation of the PI3K/AKT network"
## [21] "Constitutive Signaling by Aberrant PI3K in Cancer"
## [22] "PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling"
## [23] "Regulated Necrosis"
## [24] "MAPK1/MAPK3 signaling"
## [25] "Signaling by EGFR in Cancer"
## [26] "Selective autophagy"
## [27] "Ub-specific processing proteases"
## [28] "DNA Damage Bypass"
## [29] "Unfolded Protein Response (UPR)"
## [30] "Cellular Senescence"
## [31] "Programmed Cell Death"
## [32] "Macroautophagy"
## [33] "Potential therapeutics for SARS"
## [34] "RIPK1-mediated regulated necrosis"
## [35] "Regulation of necroptotic cell death"
## [36] "RAF/MAP kinase cascade"
## [37] "Clathrin-mediated endocytosis"
## [38] "Signaling by ERBB2 TMD/JMD mutants"
## [39] "Constitutive Signaling by Overexpressed ERBB2"
## [40] "Mitophagy"
## [41] "Senescence-Associated Secretory Phenotype (SASP)"
## [42] "Signaling by FGFR in disease"
## [43] "IRE1alpha activates chaperones"
## [44] "NOTCH3 Activation and Transmission of Signal to the Nucleus"
## [45] "Autophagy"
## [46] "Cargo recognition for clathrin-mediated endocytosis"
## [47] "Signaling by ERBB2 in Cancer"
## [48] "Regulation of TP53 Activity through Phosphorylation"
## [49] "Adaptive Immune System"
## [50] "TNF signaling"
## [51] "Deubiquitination"
## [52] "Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models"
## [53] "Neurodegenerative Diseases"
## [54] "XBP1(S) activates chaperone genes"
## [55] "Translation"
## [56] "Signaling by ERBB2 KD Mutants"
## [57] "Constitutive Signaling by AKT1 E17K in Cancer"
## [58] "Negative regulation of MET activity"
## [59] "Translesion synthesis by POLI"
## [60] "Post-translational protein modification"
## [61] "PINK1-PRKN Mediated Mitophagy"
## [62] "Translesion synthesis by POLK"
## [63] "VEGFA-VEGFR2 Pathway"
## [64] "Signaling by PDGF"
## [65] "RAC1 GTPase cycle"
## [66] "MTOR signalling"
## [67] "Cyclin D associated events in G1"
## [68] "G1 Phase"
## [69] "Regulation of TNFR1 signaling"
## [70] "Metabolism of nucleotides"
## [71] "InlB-mediated entry of Listeria monocytogenes into host cell"
## [72] "Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants"
## [73] "Signaling by Ligand-Responsive EGFR Variants in Cancer"
## [74] "COPI-dependent Golgi-to-ER retrograde traffic"
## [75] "Defective Intrinsic Pathway for Apoptosis"
## [76] "Diseases of mitotic cell cycle"
## [77] "Signaling by NTRK3 (TRKC)"
## [78] "NOTCH2 Activation and Transmission of Signal to the Nucleus"
## [79] "Chaperone Mediated Autophagy"
## [80] "Aberrant regulation of mitotic cell cycle due to RB1 defects"
## [81] "Signaling by ROBO receptors"
## [82] "Downregulation of ERBB2:ERBB3 signaling"
## [83] "Interleukin receptor SHC signaling"
## [84] "Signaling by ERBB2 ECD mutants"
## [85] "Signaling by VEGF"
## [86] "trans-Golgi Network Vesicle Budding"
## [87] "Interleukin-1 family signaling"
## [88] "Death Receptor Signalling"
## [89] "GRB2 events in ERBB2 signaling"
## [90] "APC/C:Cdc20 mediated degradation of Cyclin B"
## [91] "Signaling by FGFR"
## [92] "TP53 Regulates Metabolic Genes"
## [93] "Signaling by NOTCH"
## [94] "Transcriptional regulation by RUNX3"
## [95] "Golgi Associated Vesicle Biogenesis"
## [96] "SARS-CoV Infections"
## [97] "Signaling by KIT in disease"
## [98] "Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants"
## [99] "MAPK6/MAPK4 signaling"
## [100] "IL-6-type cytokine receptor ligand interactions"
## [101] "VEGFR2 mediated vascular permeability"
## [102] "Interconversion of nucleotide di- and triphosphates"
## [103] "EPH-Ephrin signaling"
## [104] "APC-Cdc20 mediated degradation of Nek2A"
## [105] "Golgi-to-ER retrograde transport"
## [106] "Metabolism of amino acids and derivatives"
## [107] "RAC2 GTPase cycle"
## [108] "Constitutive Signaling by NOTCH1 HD Domain Mutants"
## [109] "Signaling by NOTCH1 HD Domain Mutants in Cancer"
## [110] "Influenza Infection"
## [111] "Interleukin-6 signaling"
## [112] "Activated NOTCH1 Transmits Signal to the Nucleus"
## [113] "TNFR1-induced NFkappaB signaling pathway"
## [114] "Signaling by NOTCH3"
## [115] "Signaling by FGFR1 in disease"
## [116] "Carboxyterminal post-translational modifications of tubulin"
## [117] "Regulation of TP53 Expression and Degradation"
## [118] "RHOA GTPase cycle"
## [119] "Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways"
## [120] "Costimulation by the CD28 family"
## [121] "Kinesins"
## [122] "Syndecan interactions"
## [123] "Signaling by NOTCH2"
## [124] "SHC1 events in ERBB4 signaling"
## [125] "Listeria monocytogenes entry into host cells"
## [126] "Synthesis of active ubiquitin: roles of E1 and E2 enzymes"
## [127] "Constitutive Signaling by EGFRvIII"
## [128] "Signaling by EGFRvIII in Cancer"
## [129] "Platelet activation, signaling and aggregation"
## [130] "CTLA4 inhibitory signaling"
## [131] "EPH-ephrin mediated repulsion of cells"
## [132] "ISG15 antiviral mechanism"
## [133] "Regulation of TP53 Degradation"
## [134] "Antiviral mechanism by IFN-stimulated genes"
## [135] "ATF4 activates genes in response to endoplasmic reticulum stress"
## [136] "AKT phosphorylates targets in the cytosol"
## [137] "COPI-mediated anterograde transport"
## [138] "Regulation of expression of SLITs and ROBOs"
## [139] "Downstream signal transduction"
## [140] "Interleukin-12 signaling"
## [141] "Gap junction degradation"
## [142] "Energy dependent regulation of mTOR by LKB1-AMPK"
## [143] "RNA Polymerase II Transcription"
## [144] "FGFR1 mutant receptor activation"
## [145] "FOXO-mediated transcription"
## [146] "ERBB2 Activates PTK6 Signaling"
## [147] "Cilium Assembly"
## [148] "Interleukin-12 family signaling"# intersection
intersect(mc_up,ms)## [1] "Cell Cycle, Mitotic"
## [2] "Cell Cycle"
## [3] "Immune System"
## [4] "DNA strand elongation"
## [5] "Synthesis of DNA"
## [6] "DNA Replication"
## [7] "M Phase"
## [8] "S Phase"
## [9] "Cytokine Signaling in Immune system"
## [10] "Mitotic G1 phase and G1/S transition"
## [11] "Cell Cycle Checkpoints"
## [12] "Signaling by Interleukins"
## [13] "Signaling by Receptor Tyrosine Kinases"
## [14] "G1/S Transition"
## [15] "Nervous system development"
## [16] "Axon guidance"
## [17] "Mitotic Metaphase and Anaphase"
## [18] "Mitotic Anaphase"
## [19] "Telomere Maintenance"
## [20] "Unwinding of DNA"
## [21] "Chromosome Maintenance"
## [22] "Activation of the pre-replicative complex"
## [23] "Hemostasis"
## [24] "Interleukin-10 signaling"
## [25] "Vesicle-mediated transport"
## [26] "PCNA-Dependent Long Patch Base Excision Repair"
## [27] "Gap-filling DNA repair synthesis and ligation in GG-NER"
## [28] "Extension of Telomeres"
## [29] "Mitotic Prometaphase"
## [30] "Lagging Strand Synthesis"
## [31] "Membrane Trafficking"
## [32] "Recognition of DNA damage by PCNA-containing replication complex"
## [33] "HDR through Homologous Recombination (HRR)"
## [34] "DNA Replication Pre-Initiation"
## [35] "Response of EIF2AK1 (HRI) to heme deficiency"
## [36] "Resolution of AP sites via the multiple-nucleotide patch replacement pathway"
## [37] "G2/M Checkpoints"
## [38] "Homology Directed Repair"
## [39] "FLT3 Signaling"
## [40] "Processive synthesis on the lagging strand"
## [41] "HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)"
## [42] "Activation of ATR in response to replication stress"
## [43] "Extracellular matrix organization"
## [44] "Resolution of Abasic Sites (AP sites)"
## [45] "Cell surface interactions at the vascular wall"
## [46] "Switching of origins to a post-replicative state"
## [47] "Cholesterol biosynthesis"
## [48] "Transcriptional Regulation by TP53"
## [49] "RHO GTPase Effectors"
## [50] "L1CAM interactions"
## [51] "Metabolism"
## [52] "Telomere C-strand (Lagging Strand) Synthesis"
## [53] "Separation of Sister Chromatids"
## [54] "Removal of the Flap Intermediate"
## [55] "Base Excision Repair"
## [56] "RHO GTPases Activate Formins"
## [57] "DNA Double-Strand Break Repair"
## [58] "Formation of tubulin folding intermediates by CCT/TriC"
## [59] "APC/C-mediated degradation of cell cycle proteins"
## [60] "Regulation of mitotic cell cycle"
## [61] "Leading Strand Synthesis"
## [62] "Polymerase switching"
## [63] "Processing of Capped Intron-Containing Pre-mRNA"
## [64] "Termination of translesion DNA synthesis"
## [65] "G1/S-Specific Transcription"
## [66] "Prefoldin mediated transfer of substrate to CCT/TriC"
## [67] "Mitotic G2-G2/M phases"
## [68] "G2/M Transition"
## [69] "mRNA Splicing - Major Pathway"
## [70] "FLT3 signaling in disease"
## [71] "Mitotic Spindle Checkpoint"
## [72] "Signaling by EGFR"
## [73] "Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template"
## [74] "SHC1 events in EGFR signaling"
## [75] "Orc1 removal from chromatin"
## [76] "Nuclear Envelope (NE) Reassembly"
## [77] "Signaling by SCF-KIT"
## [78] "Signaling by MET"
## [79] "SHC1 events in ERBB2 signaling"
## [80] "Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins"
## [81] "Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding"
## [82] "Gap-filling DNA repair synthesis and ligation in TC-NER"
## [83] "Mitotic Prophase"
## [84] "MET activates PTK2 signaling"
## [85] "mRNA Splicing"
## [86] "Interleukin-4 and Interleukin-13 signaling"
## [87] "Translesion Synthesis by POLH"
## [88] "Dual Incision in GG-NER"
## [89] "Post-chaperonin tubulin folding pathway"
## [90] "APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1"
## [91] "APC/C:Cdc20 mediated degradation of mitotic proteins"
## [92] "Assembly of the pre-replicative complex"
## [93] "Interleukin-6 family signaling"
## [94] "Interleukin-2 family signaling"
## [95] "GRB2 events in EGFR signaling"
## [96] "Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal"
## [97] "Amplification of signal from the kinetochores"
## [98] "Host Interactions of HIV factors"
## [99] "Regulation of APC/C activators between G1/S and early anaphase"
## [100] "Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)"
## [101] "CDK-mediated phosphorylation and removal of Cdc6"
## [102] "Resolution of Sister Chromatid Cohesion"
## [103] "Interleukin-3, Interleukin-5 and GM-CSF signaling"
## [104] "HSF1 activation"
## [105] "Cell recruitment (pro-inflammatory response)"
## [106] "Purinergic signaling in leishmaniasis infection"
## [107] "Metabolism of RNA"
## [108] "Signaling by ERBB4"
## [109] "Regulation of PLK1 Activity at G2/M Transition"
## [110] "EML4 and NUDC in mitotic spindle formation"
## [111] "Mismatch Repair"
## [112] "Detoxification of Reactive Oxygen Species"
## [113] "EGFR downregulation"
## [114] "Condensation of Prometaphase Chromosomes"
## [115] "Negative regulation of FLT3"
## [116] "Cell-Cell communication"
## [117] "APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint"
## [118] "HIV Infection"
## [119] "Processing of DNA double-strand break ends"
## [120] "Nephrin family interactions"
## [121] "mRNA Splicing - Minor Pathway"
## [122] "Diseases of programmed cell death"
## [123] "Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)"
## [124] "Processive synthesis on the C-strand of the telomere"
## [125] "Signaling by FLT3 fusion proteins"
## [126] "Cdc20:Phospho-APC/C mediated degradation of Cyclin A"
## [127] "PTEN Regulation"
## [128] "Anchoring of the basal body to the plasma membrane"
## [129] "Initiation of Nuclear Envelope (NE) Reformation"
## [130] "AURKA Activation by TPX2"
## [131] "Dual incision in TC-NER"
## [132] "Regulation of TP53 Activity"
## [133] "Polymerase switching on the C-strand of the telomere"
## [134] "AUF1 (hnRNP D0) binds and destabilizes mRNA"
## [135] "HDR through Single Strand Annealing (SSA)"
## [136] "Influenza Viral RNA Transcription and Replication"
## [137] "Nuclear Envelope Breakdown"
## [138] "Centrosome maturation"
## [139] "Recruitment of mitotic centrosome proteins and complexes"
## [140] "Translesion synthesis by REV1"
## [141] "Non-integrin membrane-ECM interactions"
## [142] "Recruitment of NuMA to mitotic centrosomes"
## [143] "Protein folding"
## [144] "DNA Repair"
## [145] "Regulation of PTEN stability and activity"
## [146] "Homologous DNA Pairing and Strand Exchange"
## [147] "Regulation of HSF1-mediated heat shock response"
## [148] "Cellular response to starvation"
## [149] "L13a-mediated translational silencing of Ceruloplasmin expression"
## [150] "Cellular response to heat stress"
## [151] "Mitochondrial translation initiation"
## [152] "Loss of Nlp from mitotic centrosomes"
## [153] "Loss of proteins required for interphase microtubule organization from the centrosome"
## [154] "Cellular response to chemical stress"
## [155] "Response of EIF2AK4 (GCN2) to amino acid deficiency"
## [156] "Collagen formation"
## [157] "Interleukin-1 signaling"
## [158] "G0 and Early G1"
## [159] "MET promotes cell motility"
## [160] "APC/C:Cdc20 mediated degradation of Securin"
## [161] "Interleukin-15 signaling"
## [162] "Resolution of D-Loop Structures"
## [163] "The role of GTSE1 in G2/M progression after G2 checkpoint"
## [164] "Transcription-Coupled Nucleotide Excision Repair (TC-NER)"
## [165] "Condensation of Prophase Chromosomes"
## [166] "Autodegradation of Cdh1 by Cdh1:APC/C"
## [167] "Presynaptic phase of homologous DNA pairing and strand exchange"
## [168] "Cyclin A:Cdk2-associated events at S phase entry"
## [169] "Mitochondrial translation"
## [170] "Apoptosis"
## [171] "SCF(Skp2)-mediated degradation of p27/p21"
## [172] "Cap-dependent Translation Initiation"
## [173] "Eukaryotic Translation Initiation"
## [174] "Mitochondrial translation elongation"
## [175] "Signaling by NOTCH4"
## [176] "Abortive elongation of HIV-1 transcript in the absence of Tat"
## [177] "Cyclin E associated events during G1/S transition"
## [178] "Chaperonin-mediated protein folding"
## [179] "Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S"
## [180] "Transcriptional regulation by RUNX2"
## [181] "RNA Polymerase II Transcription Termination"
## [182] "Degradation of the extracellular matrix"
## [183] "G1/S DNA Damage Checkpoints"
## [184] "Mitochondrial translation termination"
## [185] "Cyclin A/B1/B2 associated events during G2/M transition"
## [186] "GTP hydrolysis and joining of the 60S ribosomal subunit"
## [187] "PERK regulates gene expression"
## [188] "Resolution of D-loop Structures through Holliday Junction Intermediates"
## [189] "Laminin interactions"
## [190] "Translation initiation complex formation"
## [191] "Pausing and recovery of Tat-mediated HIV elongation"
## [192] "Tat-mediated HIV elongation arrest and recovery"
## [193] "Removal of the Flap Intermediate from the C-strand"
## [194] "p53-Dependent G1 DNA Damage Response"
## [195] "p53-Dependent G1/S DNA damage checkpoint"
## [196] "Processing of Capped Intronless Pre-mRNA"
## [197] "CDT1 association with the CDC6:ORC:origin complex"
## [198] "Signaling by FGFR2 IIIa TM"
## [199] "Disorders of transmembrane transporters"
## [200] "Degradation of AXIN"
## [201] "HIV elongation arrest and recovery"
## [202] "Pausing and recovery of HIV elongation"
## [203] "Interleukin-20 family signaling"
## [204] "Regulation of mRNA stability by proteins that bind AU-rich elements"If we consider both strategies to be valid, then we can define the significant sets as dysregulated. We can calculate the percent sentitivity of both approaches.
all <- unique(c(ms_up,ms_dn,mc_up))
message("Sensitivity: separate only")## Sensitivity: separate only(length(ms_up)+length(ms_dn))/length(all)## [1] 0.7394366message("Sensitivity: combined only")## Sensitivity: combined onlylength(mc_up)/length(all)## [1] 0.6197183ORA with clusterprofiler
Clusterprofiler uses a hypergeometric test. Firstly I will conduct the analysis separately for up and down regulated genes and with the correct backgound (as intended by the developers).
genesets2 <- read.gmt("ReactomePathways.gmt")
de_up <- rownames(subset(de, padj<0.05 & log2FoldChange > 0))
de_up <- unique(gt[which(rownames(gt) %in% de_up),1])
de_dn <- rownames(subset(de, padj<0.05 & log2FoldChange < 0))
de_dn <- unique(gt[which(rownames(gt) %in% de_dn),1])
de_bg <- rownames(de)
de_bg <- unique(gt[which(rownames(gt) %in% de_bg),1])
o_up <- as.data.frame(enricher(gene = de_up, universe = de_bg, maxGSSize = 5000, TERM2GENE = genesets2, pAdjustMethod="fdr"))
o_up <- rownames(subset(o_up, p.adjust < 0.05))
o_dn <- as.data.frame(enricher(gene = de_dn, universe = de_bg, maxGSSize = 5000, TERM2GENE = genesets2, pAdjustMethod="fdr"))
o_dn <- rownames(subset(o_dn, p.adjust < 0.05))
o_com <- as.data.frame(enricher(gene = union(de_up,de_dn), universe = de_bg, maxGSSize = 5000, TERM2GENE = genesets2, pAdjustMethod="fdr"))
o_com <- rownames(subset(o_com, p.adjust < 0.05))
length(o_up)## [1] 89length(o_dn)## [1] 249length(o_up) + length(o_dn)## [1] 338length(o_com)## [1] 52( length(o_up) + length(o_dn) ) / length(o_com)## [1] 6.5all <- unique(c(o_up,o_dn,o_com))
message("Sensitivity: separate only")## Sensitivity: separate only(length(o_up)+length(o_dn))/length(all)## [1] 0.9825581message("Sensitivity: combined only")## Sensitivity: combined onlylength(o_com)/length(all)## [1] 0.1511628Euler diagram of the significant pathways found with each approach.
l2 <- list("sep up"=o_up,"sep dn"=o_dn,"comb"=o_com)
plot(euler(l2),quantities = TRUE, edges = "gray", main="ORA: combined vs separated")
List gene sets which are specific to each approach.
o_sep <- c(o_up,o_dn)
# in sep but not comb
setdiff(o_sep,o_com)## [1] "Response of EIF2AK4 (GCN2) to amino acid deficiency"
## [2] "Eukaryotic Translation Elongation"
## [3] "L13a-mediated translational silencing of Ceruloplasmin expression"
## [4] "Peptide chain elongation"
## [5] "GTP hydrolysis and joining of the 60S ribosomal subunit"
## [6] "Formation of a pool of free 40S subunits"
## [7] "Selenocysteine synthesis"
## [8] "Cap-dependent Translation Initiation"
## [9] "Eukaryotic Translation Initiation"
## [10] "Viral mRNA Translation"
## [11] "Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)"
## [12] "Eukaryotic Translation Termination"
## [13] "Selenoamino acid metabolism"
## [14] "SRP-dependent cotranslational protein targeting to membrane"
## [15] "Interleukin-10 signaling"
## [16] "Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)"
## [17] "Nonsense-Mediated Decay (NMD)"
## [18] "Extracellular matrix organization"
## [19] "Axon guidance"
## [20] "Cellular response to starvation"
## [21] "FOXO-mediated transcription of cell cycle genes"
## [22] "Interleukin-4 and Interleukin-13 signaling"
## [23] "Collagen formation"
## [24] "Assembly of collagen fibrils and other multimeric structures"
## [25] "Signaling by FLT3 fusion proteins"
## [26] "Response of EIF2AK1 (HRI) to heme deficiency"
## [27] "Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer"
## [28] "Signaling by FLT3 ITD and TKD mutants"
## [29] "Influenza Viral RNA Transcription and Replication"
## [30] "MET promotes cell motility"
## [31] "VEGFA-VEGFR2 Pathway"
## [32] "Signaling by VEGF"
## [33] "RAB GEFs exchange GTP for GDP on RABs"
## [34] "GRB2 events in EGFR signaling"
## [35] "Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S"
## [36] "Non-integrin membrane-ECM interactions"
## [37] "Signaling by TGFB family members"
## [38] "Signaling by SCF-KIT"
## [39] "RAC1 GTPase cycle"
## [40] "Ribosomal scanning and start codon recognition"
## [41] "Translation initiation complex formation"
## [42] "Laminin interactions"
## [43] "FOXO-mediated transcription"
## [44] "Influenza Infection"
## [45] "Interleukin-6 family signaling"
## [46] "Signaling by BMP"
## [47] "Formation of the ternary complex, and subsequently, the 43S complex"
## [48] "Signaling by EGFR"
## [49] "Cell junction organization"
## [50] "Downregulation of SMAD2/3:SMAD4 transcriptional activity"
## [51] "Signaling by CSF3 (G-CSF)"
## [52] "Developmental Biology"
## [53] "Interleukin-20 family signaling"
## [54] "MET activates PTK2 signaling"
## [55] "Netrin-1 signaling"
## [56] "Interleukin-15 signaling"
## [57] "Negative regulation of FLT3"
## [58] "SHC1 events in EGFR signaling"
## [59] "PERK regulates gene expression"
## [60] "Constitutive Signaling by Aberrant PI3K in Cancer"
## [61] "Autophagy"
## [62] "Signaling by TGF-beta Receptor Complex"
## [63] "Signaling by PDGF"
## [64] "SHC1 events in ERBB2 signaling"
## [65] "Syndecan interactions"
## [66] "Rab regulation of trafficking"
## [67] "Processing of Capped Intron-Containing Pre-mRNA"
## [68] "mRNA Splicing - Major Pathway"
## [69] "mRNA Splicing"
## [70] "G2/M Checkpoints"
## [71] "DNA Replication Pre-Initiation"
## [72] "Homology Directed Repair"
## [73] "Chromosome Maintenance"
## [74] "Switching of origins to a post-replicative state"
## [75] "HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)"
## [76] "DNA Double-Strand Break Repair"
## [77] "Orc1 removal from chromatin"
## [78] "Resolution of Abasic Sites (AP sites)"
## [79] "DNA Repair"
## [80] "APC/C-mediated degradation of cell cycle proteins"
## [81] "Regulation of mitotic cell cycle"
## [82] "Mitotic G2-G2/M phases"
## [83] "G2/M Transition"
## [84] "Mitochondrial translation elongation"
## [85] "Base Excision Repair"
## [86] "Assembly of the pre-replicative complex"
## [87] "HDR through Homologous Recombination (HRR)"
## [88] "Lagging Strand Synthesis"
## [89] "Separation of Sister Chromatids"
## [90] "Regulation of APC/C activators between G1/S and early anaphase"
## [91] "Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins"
## [92] "Resolution of AP sites via the multiple-nucleotide patch replacement pathway"
## [93] "Metabolism of RNA"
## [94] "Host Interactions of HIV factors"
## [95] "APC/C:Cdc20 mediated degradation of mitotic proteins"
## [96] "PCNA-Dependent Long Patch Base Excision Repair"
## [97] "The role of GTSE1 in G2/M progression after G2 checkpoint"
## [98] "Respiratory electron transport"
## [99] "Mitochondrial translation initiation"
## [100] "Mitochondrial translation termination"
## [101] "APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1"
## [102] "SCF(Skp2)-mediated degradation of p27/p21"
## [103] "CDK-mediated phosphorylation and removal of Cdc6"
## [104] "Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins."
## [105] "The citric acid (TCA) cycle and respiratory electron transport"
## [106] "Unwinding of DNA"
## [107] "Processive synthesis on the lagging strand"
## [108] "Mitochondrial translation"
## [109] "AUF1 (hnRNP D0) binds and destabilizes mRNA"
## [110] "Activation of ATR in response to replication stress"
## [111] "APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint"
## [112] "mRNA Splicing - Minor Pathway"
## [113] "Cdc20:Phospho-APC/C mediated degradation of Cyclin A"
## [114] "Removal of the Flap Intermediate"
## [115] "CDT1 association with the CDC6:ORC:origin complex"
## [116] "FBXL7 down-regulates AURKA during mitotic entry and in early mitosis"
## [117] "Negative regulation of NOTCH4 signaling"
## [118] "SCF-beta-TrCP mediated degradation of Emi1"
## [119] "Processing of DNA double-strand break ends"
## [120] "HSF1 activation"
## [121] "RNA Polymerase II Transcription Termination"
## [122] "Metabolism"
## [123] "Degradation of GLI2 by the proteasome"
## [124] "APC/C:Cdc20 mediated degradation of Securin"
## [125] "Transport of Mature Transcript to Cytoplasm"
## [126] "Cellular response to chemical stress"
## [127] "Autodegradation of Cdh1 by Cdh1:APC/C"
## [128] "Cholesterol biosynthesis"
## [129] "Vif-mediated degradation of APOBEC3G"
## [130] "Telomere C-strand (Lagging Strand) Synthesis"
## [131] "Regulation of ornithine decarboxylase (ODC)"
## [132] "Vpu mediated degradation of CD4"
## [133] "HIV Infection"
## [134] "GLI3 is processed to GLI3R by the proteasome"
## [135] "Cyclin A:Cdk2-associated events at S phase entry"
## [136] "Cyclin E associated events during G1/S transition"
## [137] "Autodegradation of the E3 ubiquitin ligase COP1"
## [138] "p53-Independent DNA Damage Response"
## [139] "p53-Independent G1/S DNA damage checkpoint"
## [140] "Ubiquitin Mediated Degradation of Phosphorylated Cdc25A"
## [141] "Ubiquitin-dependent degradation of Cyclin D"
## [142] "Formation of tubulin folding intermediates by CCT/TriC"
## [143] "Regulation of activated PAK-2p34 by proteasome mediated degradation"
## [144] "Degradation of GLI1 by the proteasome"
## [145] "Prefoldin mediated transfer of substrate to CCT/TriC"
## [146] "Degradation of DVL"
## [147] "Leading Strand Synthesis"
## [148] "Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)"
## [149] "Polymerase switching"
## [150] "Cross-presentation of soluble exogenous antigens (endosomes)"
## [151] "Asymmetric localization of PCP proteins"
## [152] "Transcriptional regulation by RUNX2"
## [153] "mRNA 3'-end processing"
## [154] "Regulation of HMOX1 expression and activity"
## [155] "Hh mutants are degraded by ERAD"
## [156] "Recognition of DNA damage by PCNA-containing replication complex"
## [157] "Centrosome maturation"
## [158] "Recruitment of mitotic centrosome proteins and complexes"
## [159] "Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding"
## [160] "G1/S-Specific Transcription"
## [161] "Processing of Capped Intronless Pre-mRNA"
## [162] "Transport of Mature mRNA derived from an Intron-Containing Transcript"
## [163] "Metabolism of polyamines"
## [164] "G1/S DNA Damage Checkpoints"
## [165] "Diseases of programmed cell death"
## [166] "Cellular response to heat stress"
## [167] "Regulation of HSF1-mediated heat shock response"
## [168] "Mitotic Prophase"
## [169] "Hh mutants abrogate ligand secretion"
## [170] "ROS sensing by NFE2L2"
## [171] "p53-Dependent G1 DNA Damage Response"
## [172] "p53-Dependent G1/S DNA damage checkpoint"
## [173] "Regulation of mRNA stability by proteins that bind AU-rich elements"
## [174] "Recruitment of NuMA to mitotic centrosomes"
## [175] "Degradation of AXIN"
## [176] "G2/M DNA damage checkpoint"
## [177] "Hedgehog ligand biogenesis"
## [178] "Mismatch Repair"
## [179] "Regulation of Apoptosis"
## [180] "Homologous DNA Pairing and Strand Exchange"
## [181] "Abortive elongation of HIV-1 transcript in the absence of Tat"
## [182] "Regulation of RUNX2 expression and activity"
## [183] "Regulation of RUNX3 expression and activity"
## [184] "Stabilization of p53"
## [185] "Transcription-Coupled Nucleotide Excision Repair (TC-NER)"
## [186] "Mitotic Spindle Checkpoint"
## [187] "Regulation of PTEN stability and activity"
## [188] "AURKA Activation by TPX2"
## [189] "Gap-filling DNA repair synthesis and ligation in TC-NER"
## [190] "Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal"
## [191] "Amplification of signal from the kinetochores"
## [192] "Complex I biogenesis"
## [193] "Defective CFTR causes cystic fibrosis"
## [194] "NIK-->noncanonical NF-kB signaling"
## [195] "Resolution of Sister Chromatid Cohesion"
## [196] "Global Genome Nucleotide Excision Repair (GG-NER)"
## [197] "tRNA processing in the nucleus"
## [198] "Presynaptic phase of homologous DNA pairing and strand exchange"
## [199] "Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)"
## [200] "PCP/CE pathway"
## [201] "HDR through Single Strand Annealing (SSA)"
## [202] "Nucleotide Excision Repair"
## [203] "Attenuation phase"
## [204] "Dectin-1 mediated noncanonical NF-kB signaling"
## [205] "Post-chaperonin tubulin folding pathway"
## [206] "Translesion Synthesis by POLH"
## [207] "Nuclear Envelope Breakdown"
## [208] "Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha"
## [209] "Transcriptional Regulation by TP53"
## [210] "Loss of Nlp from mitotic centrosomes"
## [211] "Loss of proteins required for interphase microtubule organization from the centrosome"
## [212] "Transport of Mature mRNAs Derived from Intronless Transcripts"
## [213] "Protein localization"
## [214] "Signaling by NOTCH4"
## [215] "Resolution of D-Loop Structures"
## [216] "UCH proteinases"
## [217] "Mitochondrial protein import"
## [218] "Regulation of PLK1 Activity at G2/M Transition"
## [219] "Activation of NF-kappaB in B cells"
## [220] "RUNX1 regulates transcription of genes involved in differentiation of HSCs"
## [221] "Metabolism of non-coding RNA"
## [222] "snRNP Assembly"
## [223] "ABC transporter disorders"
## [224] "Nuclear Envelope (NE) Reassembly"
## [225] "SUMOylation of DNA replication proteins"
## [226] "Cytoprotection by HMOX1"
## [227] "Fanconi Anemia Pathway"
## [228] "Viral Messenger RNA Synthesis"
## [229] "Metabolism of porphyrins"
## [230] "Anchoring of the basal body to the plasma membrane"
## [231] "EML4 and NUDC in mitotic spindle formation"
## [232] "Dual Incision in GG-NER"
## [233] "Transport of Mature mRNA Derived from an Intronless Transcript"
## [234] "Regulation of RAS by GAPs"
## [235] "Hedgehog 'on' state"
## [236] "Processing of Intronless Pre-mRNAs"
## [237] "Resolution of D-loop Structures through Holliday Junction Intermediates"
## [238] "Protein folding"
## [239] "Downstream signaling events of B Cell Receptor (BCR)"
## [240] "Pausing and recovery of Tat-mediated HIV elongation"
## [241] "Tat-mediated HIV elongation arrest and recovery"
## [242] "PTEN Regulation"
## [243] "Degradation of beta-catenin by the destruction complex"
## [244] "tRNA processing"
## [245] "Polymerase switching on the C-strand of the telomere"
## [246] "TNFR2 non-canonical NF-kB pathway"
## [247] "Transcriptional regulation by small RNAs"
## [248] "Interleukin-1 signaling"
## [249] "HSF1-dependent transactivation"
## [250] "Association of TriC/CCT with target proteins during biosynthesis"
## [251] "Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template"
## [252] "Folding of actin by CCT/TriC"
## [253] "Dual incision in TC-NER"
## [254] "Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol"
## [255] "Translesion synthesis by REV1"
## [256] "Heme biosynthesis"
## [257] "Deposition of new CENPA-containing nucleosomes at the centromere"
## [258] "Detoxification of Reactive Oxygen Species"
## [259] "Nucleosome assembly"
## [260] "Diseases of DNA repair"
## [261] "Rev-mediated nuclear export of HIV RNA"
## [262] "ABC-family proteins mediated transport"
## [263] "HIV elongation arrest and recovery"
## [264] "Pausing and recovery of HIV elongation"
## [265] "Termination of translesion DNA synthesis"
## [266] "Hedgehog 'off' state"
## [267] "Disorders of transmembrane transporters"
## [268] "Apoptosis"
## [269] "TCF dependent signaling in response to WNT"
## [270] "Chaperonin-mediated protein folding"
## [271] "Glucose metabolism"
## [272] "DNA Damage Bypass"
## [273] "Transport of the SLBP Dependant Mature mRNA"
## [274] "Processive synthesis on the C-strand of the telomere"
## [275] "Translesion synthesis by POLI"
## [276] "Translesion synthesis by POLK"
## [277] "Ub-specific processing proteases"
## [278] "ER-Phagosome pathway"
## [279] "Formation of the Early Elongation Complex"
## [280] "Formation of the HIV-1 Early Elongation Complex"
## [281] "G0 and Early G1"
## [282] "Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)"
## [283] "Purine catabolism"
## [284] "Defective pyroptosis"
## [285] "Condensation of Prometaphase Chromosomes"
## [286] "Cellular response to hypoxia"
## [287] "Interactions of Rev with host cellular proteins"
## [288] "Regulation of TP53 Activity"
## [289] "Potential therapeutics for SARS"
## [290] "E2F mediated regulation of DNA replication"
## [291] "Transport of the SLBP independent Mature mRNA"
## [292] "Signaling by NOTCH"# in comb but not sep
setdiff(o_com,o_sep)## [1] "Signaling by Rho GTPases, Miro GTPases and RHOBTB3"
## [2] "Signaling by Rho GTPases"
## [3] "Disease"
## [4] "Downregulation of ERBB2 signaling"
## [5] "Selective autophagy"
## [6] "Cell surface interactions at the vascular wall"# intersection
intersect(mc_up,ms)## [1] "Cell Cycle, Mitotic"
## [2] "Cell Cycle"
## [3] "Immune System"
## [4] "DNA strand elongation"
## [5] "Synthesis of DNA"
## [6] "DNA Replication"
## [7] "M Phase"
## [8] "S Phase"
## [9] "Cytokine Signaling in Immune system"
## [10] "Mitotic G1 phase and G1/S transition"
## [11] "Cell Cycle Checkpoints"
## [12] "Signaling by Interleukins"
## [13] "Signaling by Receptor Tyrosine Kinases"
## [14] "G1/S Transition"
## [15] "Nervous system development"
## [16] "Axon guidance"
## [17] "Mitotic Metaphase and Anaphase"
## [18] "Mitotic Anaphase"
## [19] "Telomere Maintenance"
## [20] "Unwinding of DNA"
## [21] "Chromosome Maintenance"
## [22] "Activation of the pre-replicative complex"
## [23] "Hemostasis"
## [24] "Interleukin-10 signaling"
## [25] "Vesicle-mediated transport"
## [26] "PCNA-Dependent Long Patch Base Excision Repair"
## [27] "Gap-filling DNA repair synthesis and ligation in GG-NER"
## [28] "Extension of Telomeres"
## [29] "Mitotic Prometaphase"
## [30] "Lagging Strand Synthesis"
## [31] "Membrane Trafficking"
## [32] "Recognition of DNA damage by PCNA-containing replication complex"
## [33] "HDR through Homologous Recombination (HRR)"
## [34] "DNA Replication Pre-Initiation"
## [35] "Response of EIF2AK1 (HRI) to heme deficiency"
## [36] "Resolution of AP sites via the multiple-nucleotide patch replacement pathway"
## [37] "G2/M Checkpoints"
## [38] "Homology Directed Repair"
## [39] "FLT3 Signaling"
## [40] "Processive synthesis on the lagging strand"
## [41] "HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)"
## [42] "Activation of ATR in response to replication stress"
## [43] "Extracellular matrix organization"
## [44] "Resolution of Abasic Sites (AP sites)"
## [45] "Cell surface interactions at the vascular wall"
## [46] "Switching of origins to a post-replicative state"
## [47] "Cholesterol biosynthesis"
## [48] "Transcriptional Regulation by TP53"
## [49] "RHO GTPase Effectors"
## [50] "L1CAM interactions"
## [51] "Metabolism"
## [52] "Telomere C-strand (Lagging Strand) Synthesis"
## [53] "Separation of Sister Chromatids"
## [54] "Removal of the Flap Intermediate"
## [55] "Base Excision Repair"
## [56] "RHO GTPases Activate Formins"
## [57] "DNA Double-Strand Break Repair"
## [58] "Formation of tubulin folding intermediates by CCT/TriC"
## [59] "APC/C-mediated degradation of cell cycle proteins"
## [60] "Regulation of mitotic cell cycle"
## [61] "Leading Strand Synthesis"
## [62] "Polymerase switching"
## [63] "Processing of Capped Intron-Containing Pre-mRNA"
## [64] "Termination of translesion DNA synthesis"
## [65] "G1/S-Specific Transcription"
## [66] "Prefoldin mediated transfer of substrate to CCT/TriC"
## [67] "Mitotic G2-G2/M phases"
## [68] "G2/M Transition"
## [69] "mRNA Splicing - Major Pathway"
## [70] "FLT3 signaling in disease"
## [71] "Mitotic Spindle Checkpoint"
## [72] "Signaling by EGFR"
## [73] "Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template"
## [74] "SHC1 events in EGFR signaling"
## [75] "Orc1 removal from chromatin"
## [76] "Nuclear Envelope (NE) Reassembly"
## [77] "Signaling by SCF-KIT"
## [78] "Signaling by MET"
## [79] "SHC1 events in ERBB2 signaling"
## [80] "Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins"
## [81] "Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding"
## [82] "Gap-filling DNA repair synthesis and ligation in TC-NER"
## [83] "Mitotic Prophase"
## [84] "MET activates PTK2 signaling"
## [85] "mRNA Splicing"
## [86] "Interleukin-4 and Interleukin-13 signaling"
## [87] "Translesion Synthesis by POLH"
## [88] "Dual Incision in GG-NER"
## [89] "Post-chaperonin tubulin folding pathway"
## [90] "APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1"
## [91] "APC/C:Cdc20 mediated degradation of mitotic proteins"
## [92] "Assembly of the pre-replicative complex"
## [93] "Interleukin-6 family signaling"
## [94] "Interleukin-2 family signaling"
## [95] "GRB2 events in EGFR signaling"
## [96] "Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal"
## [97] "Amplification of signal from the kinetochores"
## [98] "Host Interactions of HIV factors"
## [99] "Regulation of APC/C activators between G1/S and early anaphase"
## [100] "Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)"
## [101] "CDK-mediated phosphorylation and removal of Cdc6"
## [102] "Resolution of Sister Chromatid Cohesion"
## [103] "Interleukin-3, Interleukin-5 and GM-CSF signaling"
## [104] "HSF1 activation"
## [105] "Cell recruitment (pro-inflammatory response)"
## [106] "Purinergic signaling in leishmaniasis infection"
## [107] "Metabolism of RNA"
## [108] "Signaling by ERBB4"
## [109] "Regulation of PLK1 Activity at G2/M Transition"
## [110] "EML4 and NUDC in mitotic spindle formation"
## [111] "Mismatch Repair"
## [112] "Detoxification of Reactive Oxygen Species"
## [113] "EGFR downregulation"
## [114] "Condensation of Prometaphase Chromosomes"
## [115] "Negative regulation of FLT3"
## [116] "Cell-Cell communication"
## [117] "APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint"
## [118] "HIV Infection"
## [119] "Processing of DNA double-strand break ends"
## [120] "Nephrin family interactions"
## [121] "mRNA Splicing - Minor Pathway"
## [122] "Diseases of programmed cell death"
## [123] "Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)"
## [124] "Processive synthesis on the C-strand of the telomere"
## [125] "Signaling by FLT3 fusion proteins"
## [126] "Cdc20:Phospho-APC/C mediated degradation of Cyclin A"
## [127] "PTEN Regulation"
## [128] "Anchoring of the basal body to the plasma membrane"
## [129] "Initiation of Nuclear Envelope (NE) Reformation"
## [130] "AURKA Activation by TPX2"
## [131] "Dual incision in TC-NER"
## [132] "Regulation of TP53 Activity"
## [133] "Polymerase switching on the C-strand of the telomere"
## [134] "AUF1 (hnRNP D0) binds and destabilizes mRNA"
## [135] "HDR through Single Strand Annealing (SSA)"
## [136] "Influenza Viral RNA Transcription and Replication"
## [137] "Nuclear Envelope Breakdown"
## [138] "Centrosome maturation"
## [139] "Recruitment of mitotic centrosome proteins and complexes"
## [140] "Translesion synthesis by REV1"
## [141] "Non-integrin membrane-ECM interactions"
## [142] "Recruitment of NuMA to mitotic centrosomes"
## [143] "Protein folding"
## [144] "DNA Repair"
## [145] "Regulation of PTEN stability and activity"
## [146] "Homologous DNA Pairing and Strand Exchange"
## [147] "Regulation of HSF1-mediated heat shock response"
## [148] "Cellular response to starvation"
## [149] "L13a-mediated translational silencing of Ceruloplasmin expression"
## [150] "Cellular response to heat stress"
## [151] "Mitochondrial translation initiation"
## [152] "Loss of Nlp from mitotic centrosomes"
## [153] "Loss of proteins required for interphase microtubule organization from the centrosome"
## [154] "Cellular response to chemical stress"
## [155] "Response of EIF2AK4 (GCN2) to amino acid deficiency"
## [156] "Collagen formation"
## [157] "Interleukin-1 signaling"
## [158] "G0 and Early G1"
## [159] "MET promotes cell motility"
## [160] "APC/C:Cdc20 mediated degradation of Securin"
## [161] "Interleukin-15 signaling"
## [162] "Resolution of D-Loop Structures"
## [163] "The role of GTSE1 in G2/M progression after G2 checkpoint"
## [164] "Transcription-Coupled Nucleotide Excision Repair (TC-NER)"
## [165] "Condensation of Prophase Chromosomes"
## [166] "Autodegradation of Cdh1 by Cdh1:APC/C"
## [167] "Presynaptic phase of homologous DNA pairing and strand exchange"
## [168] "Cyclin A:Cdk2-associated events at S phase entry"
## [169] "Mitochondrial translation"
## [170] "Apoptosis"
## [171] "SCF(Skp2)-mediated degradation of p27/p21"
## [172] "Cap-dependent Translation Initiation"
## [173] "Eukaryotic Translation Initiation"
## [174] "Mitochondrial translation elongation"
## [175] "Signaling by NOTCH4"
## [176] "Abortive elongation of HIV-1 transcript in the absence of Tat"
## [177] "Cyclin E associated events during G1/S transition"
## [178] "Chaperonin-mediated protein folding"
## [179] "Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S"
## [180] "Transcriptional regulation by RUNX2"
## [181] "RNA Polymerase II Transcription Termination"
## [182] "Degradation of the extracellular matrix"
## [183] "G1/S DNA Damage Checkpoints"
## [184] "Mitochondrial translation termination"
## [185] "Cyclin A/B1/B2 associated events during G2/M transition"
## [186] "GTP hydrolysis and joining of the 60S ribosomal subunit"
## [187] "PERK regulates gene expression"
## [188] "Resolution of D-loop Structures through Holliday Junction Intermediates"
## [189] "Laminin interactions"
## [190] "Translation initiation complex formation"
## [191] "Pausing and recovery of Tat-mediated HIV elongation"
## [192] "Tat-mediated HIV elongation arrest and recovery"
## [193] "Removal of the Flap Intermediate from the C-strand"
## [194] "p53-Dependent G1 DNA Damage Response"
## [195] "p53-Dependent G1/S DNA damage checkpoint"
## [196] "Processing of Capped Intronless Pre-mRNA"
## [197] "CDT1 association with the CDC6:ORC:origin complex"
## [198] "Signaling by FGFR2 IIIa TM"
## [199] "Disorders of transmembrane transporters"
## [200] "Degradation of AXIN"
## [201] "HIV elongation arrest and recovery"
## [202] "Pausing and recovery of HIV elongation"
## [203] "Interleukin-20 family signaling"
## [204] "Regulation of mRNA stability by proteins that bind AU-rich elements"Euler diagrams comparing FCS and ORA methods
par(cex.main=0.5)
par(mar=c(2,2,2,2))
l3 <- list("ORA up"=o_up,"ORA dn"=o_dn,"ORA comb"=o_com,
"FCS up"=ms_up,"FCS dn"=ms_dn,"FCS comb"=mc_up)
plot(euler(l3),quantities = TRUE, edges = "gray", main="FCS compared to ORA")
Save data
dat <- list( "FCS_up"=ms_up,
"FCS_dn"=ms_dn,
"FCS_com"=mc_up,
"ORA_up"= o_up,
"ORA_dn"=o_dn,
"ORA_com"=o_com)
str(dat)## List of 6
## $ FCS_up : chr [1:98] "Response of EIF2AK4 (GCN2) to amino acid deficiency" "Eukaryotic Translation Elongation" "Peptide chain elongation" "Viral mRNA Translation" ...
## $ FCS_dn : chr [1:322] "Cell Cycle" "Cell Cycle, Mitotic" "DNA Replication" "Synthesis of DNA" ...
## $ FCS_com: chr [1:352] "Cell Cycle, Mitotic" "Cell Cycle" "Immune System" "Signal Transduction" ...
## $ ORA_up : chr [1:89] "Response of EIF2AK4 (GCN2) to amino acid deficiency" "Eukaryotic Translation Elongation" "L13a-mediated translational silencing of Ceruloplasmin expression" "Peptide chain elongation" ...
## $ ORA_dn : chr [1:249] "Cell Cycle" "Cell Cycle, Mitotic" "DNA Replication" "Synthesis of DNA" ...
## $ ORA_com: chr [1:52] "Cell Cycle, Mitotic" "Cell Cycle" "FLT3 Signaling" "Signaling by Rho GTPases, Miro GTPases and RHOBTB3" ...saveRDS(dat,file = "ex6dat.rds")Conclusion
For mitch, it would appear that performing direction informed (DI) analysis clearly yields more differentially regulated pathways (413) as compared to the direction agnostic (DA) method (55).
That being said, there were 18 pathways identified only in the DA method that appeared to be related to the physiology of the model. These gene sets are likely to contain a mix of genes affected by the stimulus in different ways - for example a mix of up and downregulated genes. Are these really real? Not sure.
This pattern was consistent with ORA, where 80 sets were identified with separate analysis and only 23 with the combined analysis.
When comparing ORA to FCS, we found that FCS identified many more sets than ORA. In fact all gene sets that were identified by ORA were also identified by FCS, except for 3 that were specific to the ORA up set.
Let’s look at those now.
myfcs <- c(ms_up, mc_up)
setdiff(o_up,myfcs)## [1] "Signaling by TGFB family members"
## [2] "Signaling by CSF3 (G-CSF)"
## [3] "Signaling by TGF-beta Receptor Complex"
## [4] "Rab regulation of trafficking"Session information
sessionInfo()## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] eulerr_6.1.1 mitch_1.4.1
## [3] clusterProfiler_4.0.5 DESeq2_1.32.0
## [5] SummarizedExperiment_1.22.0 Biobase_2.52.0
## [7] MatrixGenerics_1.4.3 matrixStats_0.61.0
## [9] GenomicRanges_1.44.0 GenomeInfoDb_1.28.4
## [11] IRanges_2.26.0 S4Vectors_0.30.2
## [13] BiocGenerics_0.38.0 getDEE2_1.2.0
## [15] beeswarm_0.4.0 kableExtra_1.3.4
##
## loaded via a namespace (and not attached):
## [1] shadowtext_0.1.1 fastmatch_1.1-3 systemfonts_1.0.3
## [4] plyr_1.8.6 igraph_1.2.11 lazyeval_0.2.2
## [7] polylabelr_0.2.0 splines_4.1.2 BiocParallel_1.26.2
## [10] ggplot2_3.3.5 digest_0.6.29 yulab.utils_0.0.4
## [13] htmltools_0.5.2 GOSemSim_2.18.1 viridis_0.6.2
## [16] GO.db_3.13.0 fansi_1.0.0 magrittr_2.0.1
## [19] memoise_2.0.1 Biostrings_2.60.2 annotate_1.70.0
## [22] graphlayouts_0.8.0 svglite_2.0.0 enrichplot_1.12.3
## [25] colorspace_2.0-2 blob_1.2.2 rvest_1.0.2
## [28] ggrepel_0.9.1 xfun_0.29 dplyr_1.0.7
## [31] crayon_1.4.2 RCurl_1.98-1.5 jsonlite_1.7.2
## [34] scatterpie_0.1.7 genefilter_1.74.1 survival_3.2-13
## [37] ape_5.6-1 glue_1.6.0 polyclip_1.10-0
## [40] gtable_0.3.0 zlibbioc_1.38.0 XVector_0.32.0
## [43] webshot_0.5.2 htm2txt_2.1.1 DelayedArray_0.18.0
## [46] scales_1.1.1 DOSE_3.18.3 DBI_1.1.2
## [49] GGally_2.1.2 Rcpp_1.0.7 viridisLite_0.4.0
## [52] xtable_1.8-4 gridGraphics_0.5-1 tidytree_0.3.7
## [55] bit_4.0.4 htmlwidgets_1.5.4 httr_1.4.2
## [58] fgsea_1.18.0 gplots_3.1.1 RColorBrewer_1.1-2
## [61] ellipsis_0.3.2 reshape_0.8.8 pkgconfig_2.0.3
## [64] XML_3.99-0.8 farver_2.1.0 sass_0.4.0
## [67] locfit_1.5-9.4 utf8_1.2.2 later_1.3.0
## [70] ggplotify_0.1.0 tidyselect_1.1.1 rlang_0.4.12
## [73] reshape2_1.4.4 AnnotationDbi_1.54.1 munsell_0.5.0
## [76] tools_4.1.2 cachem_1.0.6 downloader_0.4
## [79] generics_0.1.1 RSQLite_2.2.9 evaluate_0.14
## [82] stringr_1.4.0 fastmap_1.1.0 yaml_2.2.1
## [85] ggtree_3.0.4 knitr_1.37 bit64_4.0.5
## [88] tidygraph_1.2.0 caTools_1.18.2 purrr_0.3.4
## [91] KEGGREST_1.32.0 ggraph_2.0.5 nlme_3.1-153
## [94] mime_0.12 aplot_0.1.2 DO.db_2.9
## [97] xml2_1.3.3 compiler_4.1.2 rstudioapi_0.13
## [100] png_0.1-7 treeio_1.16.2 tibble_3.1.6
## [103] tweenr_1.0.2 geneplotter_1.70.0 bslib_0.3.1
## [106] stringi_1.7.6 highr_0.9 lattice_0.20-45
## [109] Matrix_1.4-0 vctrs_0.3.8 pillar_1.6.4
## [112] lifecycle_1.0.1 jquerylib_0.1.4 data.table_1.14.2
## [115] cowplot_1.1.1 bitops_1.0-7 httpuv_1.6.5
## [118] patchwork_1.1.1 qvalue_2.24.0 R6_2.5.1
## [121] promises_1.2.0.1 KernSmooth_2.23-20 echarts4r_0.4.3
## [124] gridExtra_2.3 gtools_3.9.2 MASS_7.3-54
## [127] assertthat_0.2.1 GenomeInfoDbData_1.2.6 grid_4.1.2
## [130] ggfun_0.0.4 tidyr_1.1.4 rmarkdown_2.11
## [133] ggforce_0.3.3 shiny_1.7.1