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[{"$nulls":22},"RPA2",{"$nulls":4},"PSMC2",null,"MXD3"]
[{"$nulls":22},"RPA3",{"$nulls":4},"PSMC3",null,"MYB"]
[{"$nulls":22},"RPS27A",{"$nulls":4},"PSMC4",null,"MYBL2"]
[{"$nulls":22},"SKP1",{"$nulls":4},"PSMC5",null,"MYC"]
[{"$nulls":22},"SKP2",{"$nulls":4},"PSMC6",null,"MYCN"]
[{"$nulls":22},"UBA52",{"$nulls":4},"PSMD1",null,"NEK2"]
[{"$nulls":22},"UBB",{"$nulls":4},"PSMD2",null,"NPAT"]
[{"$nulls":22},"UBC",{"$nulls":4},"CASC5",null,"NRP1"]
[{"$nulls":22},"WEE1",{"$nulls":4},"PSMD3",null,"PAC1"]
[{"$nulls":27},"PSMD4",null,"PBK"]
[{"$nulls":27},"PSMD5",null,"PCNA"]
[{"$nulls":27},"NUP107",null,"PFKFB2"]
[{"$nulls":27},"PSMD7",null,"PLAU"]
[{"$nulls":27},"PSMD8",null,"PLK1"]
[{"$nulls":27},"PSMD9",null,"PMAIP1"]
[{"$nulls":27},"PSMD10",null,"PNRC2"]
[{"$nulls":27},"PSMD11",null,"POLA"]
[{"$nulls":27},"PSMD12",null,"PPARG"]
[{"$nulls":27},"PSMD13",null,"PPP1R13B"]
[{"$nulls":27},"PSME1",null,"PRKDC"]
[{"$nulls":27},"PSME2",null,"PSMA4"]
[{"$nulls":27},"SPC25",null,"PTGS2"]
[{"$nulls":27},"TAOK1",null,"PURALPHA"]
[{"$nulls":27},"RAD21",null,"RAD51AP1"]
[{"$nulls":27},"RANBP2",null,"RAD54L"]
[{"$nulls":27},"RANGAP1",null,"RBBP4"]
[{"$nulls":27},"RPA1",null,"RBBP8"]
[{"$nulls":27},"RPA2",null,"RBL1"]
[{"$nulls":27},"RPA3",null,"RBM25"]
[{"$nulls":27},"RPS27",null,"RFC5"]
[{"$nulls":27},"RPS27A",null,"RPA2"]
[{"$nulls":27},"CLIP1",null,"RPL32"]
[{"$nulls":27},"SEC13",null,"RPL8"]
[{"$nulls":27},"CENPK",null,"RQCD1"]
[{"$nulls":27},"GORASP1",null,"RRM1"]
[{"$nulls":27},"CENPH",null,"RRM2"]
[{"$nulls":27},"BUB1",null,"SERPINE1"]
[{"$nulls":27},"BUB1B",null,"SIVA"]
[{"$nulls":27},"UBA52",null,"SKP2"]
[{"$nulls":27},"UBB",null,"SLC25A14"]
[{"$nulls":27},"UBC",null,"SLC3A2"]
[{"$nulls":27},"XPO1",null,"SNRPE"]
[{"$nulls":27},"MIS12",null,"SNX19"]
[{"$nulls":27},"CENPM",null,"SOAT2"]
[{"$nulls":27},"NUP37",null,"SPAG7"]
[{"$nulls":27},"CENPO",null,"SRPR"]
[{"$nulls":27},"MLF1IP",null,"SSR4"]
[{"$nulls":27},"NUP85",null,"STMN1"]
[{"$nulls":27},"DSN1",null,"SUZ12"]
[{"$nulls":27},"CENPT",null,"TERT"]
[{"$nulls":27},"B9D2",null,"THEM2"]
[{"$nulls":27},"NDEL1",null,"TK1"]
[{"$nulls":27},"CDT1",null,"TOP2A"]
[{"$nulls":27},"SEH1L",null,"TOPBP1"]
[{"$nulls":27},"KIF18A",null,"TP53"]
[{"$nulls":27},"SMC1A",null,"TP53BP2"]
[{"$nulls":27},"CDC7",null,"TP53INP1"]
[{"$nulls":27},"CDC45L",null,"TP73"]
[{"$nulls":27},"NUF2",null,"TRIM55"]
[{"$nulls":27},"MAD1L1",null,"TUBA3"]
[{"$nulls":27},"MCM8",null,"TYMS"]
[{"$nulls":27},"KIF2B",null,"UBB"]
[{"$nulls":27},"SMC3",null,"UDG"]
[{"$nulls":27},"CENPL",null,"UHRF1"]
[{"$nulls":27},"ZW10",null,"UXT"]
[{"$nulls":27},"BUB3",null,"WDR36"]
[{"$nulls":27},"AURKB",null,"WWOX"]
[{"$nulls":27},"PSMF1",null,"ZNF451"]
[{"$nulls":27},"KIF23",null,"ZNF83"]
[{"$nulls":27},"KNTC1"]
[{"$nulls":27},"CKAP5"]
[{"$nulls":27},"PSMD6"]
[{"$nulls":27},"CDC6"]
[{"$nulls":27},"CDC20"]
[{"$nulls":27},"REC8"]

{"sheet":"Pathways sources","index":1,"n_rows":40,"n_cols":5,"rows_kept":40,"cut":false,"hidden":false,"merged":[[1,0,1,4],[11,0,11,4],[29,0,29,4]],"flags":["formulas_cached_only"]}
[]
["DDR Pathway"]
["SUBPATHWAYS","NUMBER OF GENES  Mα","DATABASE NAME","DATABASE SOURCE","NCI"]
["Base Excision Repair",44,"Ontocancro","http://www.ontocancro.org/previous/id_Ontocancro.php?ref=id_Ontocancro_base-excision-repair--ber"]
["Fanconi Anemia Pathway",24,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=419524&ID=419524","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500068&pathway_name=Fanconi%20Anemia%20pathway&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Homologous Recombination",34,"Ontocancro","http://www.ontocancro.org/previous/id_Ontocancro.php?ref=id_Ontocancro_homologous-recombination--hr"]
["Mismatch Repair",28,"Ontocancro","http://www.ontocancro.org/previous/id_Ontocancro.php?ref=id_Ontocancro_mismatch-excision-repair--mmr"]
["Nucleotide Excision Repair",51,"Ontocancro","http://www.ontocancro.org/previous/id_Ontocancro.php?ref=id_Ontocancro_nucleotide-excision-repair--ner"]
["Non-Homologous end Joining",14,"Ontocancro","http://www.ontocancro.org/previous/id_Ontocancro.php?ref=id_Ontocancro_non-homologous-end-joining"]
["Double-Strand Break Repair",22,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=419524&ID=419524","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500040&pathway_name=Double-Strand%20Break%20Repair&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
[]
["Apoptosis / Senescence Pathway"]
["SUBPATHWAYS","NUMBER OF GENES Mα ","DATABASE NAME","DATABASE SOURCE","NCI"]
["tnfr1 Signaling Pathway",14,"BioCarta","http://www.biocarta.com/pathfiles/h_tnfr1Pathway.asp","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=100015&pathway_name=tnfr1%20signaling%20pathway&source=BioCarta%20Imported&what=graphic&jpg=on&ppage=1"]
["tnfr2 Signaling Pathway",10,"BioCarta","http://www.biocarta.com/pathfiles/h_tnfr2Pathway.asp","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=100014&pathway_name=tnfr2%20signaling%20pathway&source=BioCarta%20Imported&what=graphic&jpg=on&ppage=1"]
["TNF Receptor Signaling Pathway",40,"NCI-Nature",null,"http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=tnfpathway&pathway_name=TNF%20receptor%20signaling%20pathway&source=NCI-Nature%20curated&what=graphic&jpg=on&ppage=1"]
["Death Receptor Signalling",13,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=109607&ID=73887","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500254&pathway_name=Death%20Receptor%20%20Signalling&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Apoptotic Signaling in Response to DNA Damage",13,"BioCarta","http://www.biocarta.com/pathfiles/h_chemicalPathway.asp","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=100204&pathway_name=apoptotic%20signaling%20in%20response%20to%20dna%20damage&source=BioCarta%20Imported&what=graphic&jpg=on&ppage=1"]
["Induction of apoptosis through dr3 and dr4/5 death receptors",22,"BioCarta","http://www.biocarta.com/pathfiles/h_deathPathway.asp","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=100189&pathway_name=induction%20of%20apoptosis%20through%20dr3%20and%20dr4/5%20death%20receptors&source=BioCarta%20Imported&what=graphic&jpg=on&ppage=1"]
["Apoptosis - Homo sapiens (KEGG)",83,"Kegg","http://www.ontocancro.org/previous/id_keggPathways.php?ref=id_Kegg_apoptosis---homo-sapiens--human"]
["Caspase Cascade in Apoptosis",52,"Ontocancro","http://www.ontocancro.org/previous/id_NCIPathway.php?ref=id_NCIPathway_200065"]
["Intrinsic Pathway for Apoptosis",29,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=109606&ID=109606","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500258&pathway_name=Intrinsic%20Pathway%20for%20Apoptosis&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Regulation of Apoptosis",60,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=169911&ID=169911","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500277&pathway_name=Regulation%20of%20Apoptosis&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Apoptotic Execution  Phase",52,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=75153&ID=75153","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500269&pathway_name=Apoptotic%20execution%20%20phase&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Extrinsic Pathway for Apoptosis",13,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=109607&ID=109607","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500253&pathway_name=Extrinsic%20Pathway%20for%20Apoptosis&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Granzyme A Mediated Apoptosis Pathway",14,"BioCarta","http://www.biocarta.com/pathfiles/h_setPathway.asp","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=100035&pathway_name=granzyme%20a%20mediated%20apoptosis%20pathway&source=BioCarta%20Imported&what=graphic&jpg=on&ppage=1"]
["Replicative Senescence",54,"Gene Ontology","http://ontocancro.inf.ufsm.br/index.php?pag=menuPathways"]
["NFKB Activation Pathway",20,"Ontocancro","http://ontocancro.inf.ufsm.br/index.php?pag=menuPathways"]
[]
["Cell Cycle Pathway"]
["SUBPATHWAYS","NUMBER OF GENES Mα","DATABASE NAME","DATABASE SOURCE","NCI"]
["Cell Cycle: G1/S Check Point",22,"BioCarta","http://www.biocarta.com/pathfiles/h_g1Pathway.asp","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=100160&pathway_name=cell%20cycle:%20g1/s%20check%20point&source=BioCarta%20Imported&what=graphic&jpg=on&ppage=1"]
["S Phase",112,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=69242&ID=69242","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500870&pathway_name=S%20Phase&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Cyclins and Cell Cycle Regulation",18,"BioCarta","http://www.biocarta.com/pathfiles/h_cellcyclePathway.asp","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=100207&pathway_name=cyclins%20and%20cell%20cycle%20regulation&source=BioCarta%20Imported&what=graphic&jpg=on&ppage=1"]
["G1/S DNA Damage Checkpoints",60,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=69620&ID=69615","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500313&pathway_name=G1/S%20DNA%20Damage%20Checkpoints&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["G2/M Checkpoints",43,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=69620&ID=69481","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500874&pathway_name=G2/M%20Checkpoints&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Mitotic G2-G2/M Phases",86,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=453274&ID=453274","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500915&pathway_name=Mitotic%20G2-G2/M%20phases&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Mitotic M-M/G1 Phases",178,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=453277&ID=453277","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=501008&pathway_name=Mitotic%20M-M/G1%20phases&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["Mitotic Spindle Checkpoint",19,"Reactome","http://www.reactome.org/entitylevelview/PathwayBrowser.html#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=69620&ID=69618","http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=500320&pathway_name=Mitotic%20Spindle%20Checkpoint&source=Reactome%20Imported&what=graphic&jpg=on&ppage=1"]
["RB/E2F Pathway",172,"BioCarta"]

{"sheet":"T. histologies and sources","index":2,"n_rows":12,"n_cols":5,"rows_kept":12,"cut":false,"hidden":false,"merged":[],"flags":["formulas_cached_only"]}
["Diseases","Serie","Plataform","Number of Samples","References - GEO"]
["Colonrectal Inflammation","GSE4183","Affymetrix Human Genome U133 Plus 2.0 Array - GPL 570","15 inflammation and 8 controls","http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4183"]
[]
["Colonrectal Adenoma","GSE4183","Affymetrix Human Genome U133 Plus 2.0 Array - GPL 570","15 adenomas and 8 controls","http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4183"]
["Adrenocortical Adenoma","GSE10927","Affymetrix Human Genome U133 Plus 2.0 Array - GPL 570","22 adenomas and 10 controls","http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10927"]
["PancreaS Adenoma","GSE19650","Affymetrix Human Genome U133 Plus 2.0 Array - GPL 570","6 adenomas and 7 controls","http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19650"]
["Thyroid Adenoma","GSE27155","Affymetrix Human Genome U133A Plus 2.0 Array - GPL 96","17 follicular adenomas and 4 controls","http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE27155"]
[]
["Colonrectal Carcinoma","GSE4183","Affymetrix Human Genome U133 Plus 2.0 Array - GPL 570","15 cancinomas and 8 controls","http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4183"]
["Adrenocortical Carcinoma","GSE10927","Affymetrix Human Genome U133 Plus 2.0 Array - GPL 570","33 carcinomas and  10 controls","http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10927"]
["Pancreas Carcinoma","GSE19650","Affymetrix Human Genome U133 Plus 2.0 Array - GPL 570","6 carcinomas and 7 controls","http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19650"]
["Thyroid Carcinoma","GSE27155","Affymetrix Human Genome U133A Plus 2.0 Array - GPL 96","13 follicular carcinomas and  4 controls","http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE27155"]

{"sheet":"R Script - DEG Analysis","index":3,"n_rows":42,"n_cols":1,"rows_kept":42,"cut":false,"hidden":false,"merged":[],"flags":["formulas_cached_only"]}
["library(\"limma\");library(\"Biobase\");library(\"annaffy\");library(\"hgu133plus2.db\")"]
["# fold function"]
["fold <- function(mat,pc,pa) {"]
["  change <- apply(mat[,pa],1,mean)/apply(mat[,pc],1,mean)"]
["return(change)"]
["}"]
[]
["# load gene expression matrix"]
["setwd(\"Dir/GSE4183\")  # Use directory"]
["load(\"GSE4183.RData\")"]
["samples <- pData(GSE4183_RMA)"]
["normal <- samples [1:8,]"]
["adenoma <- samples [9:23,]"]
["cancer <- samples [24:38,]"]
["inflama <- samples [39:53,]"]
["mat <- exprs(GSE4183_RMA)[, c(normal,adenoma,cancer,inflama)]"]
["colnames(mat)<- c(rep(\"normal\",length(normal)),rep(\"adenoma\",length(adenoma)),rep(\"cancer\",length(cancer)),rep(\"inflama\",length(inflama)))"]
[]
["# calculate fold change sub-expression matrix (pathway) "]
["setwd(\"Dir/GSE4183\") #Use directory"]
["filenames <- list.files(pattern=\"*.txt\")"]
["for (i in 1:length(filenames)) {"]
["  via <- read.table(filenames[i], header=TRUE,skip=2)"]
["  rownames(via) <- via$Affymetrics"]
["  # select sub gene matriz"]
["  submat <- mat[rownames(via),]"]
["  condfac <- as.factor(colnames(submat))"]
["  mn <- apply(submat[,condfac[condfac==\"normal\"]],1,mean)"]
["  ma <- apply(submat[,condfac[condfac==\"adenoma\"]],1,mean)"]
["  mc <- apply(submat[,condfac[condfac==\"cancer\"]],1,mean) "]
["  fcc <- fold(submat,condfac[condfac==\"normal\"],condfac[condfac==\"cancer\"])"]
["  fca <- fold(submat,condfac[condfac==\"normal\"],condfac[condfac==\"adenoma\"])"]
["  viaok <- cbind(cbind(cbind(cbind(cbind(via,mn),ma),mc),fca),fcc)"]
["  idx <- rownames(viaok[order(viaok$fca, decreasing=TRUE),])"]
["   write.table(viaok[idx,],file=paste(filenames[i],\"_OK.xls\"),sep=\"\\t\",col.names=NA) "]
["  "]
["  # barplot top-5  "]
["  pagesToOutputOn = 1"]
["  pdf(file=paste(filenames[i],\"_OK.pdf\",sep=\"\"), paper=\"special\",pointsize=10, width=29.7/2.54, height=20.9/2.54 * pagesToOutputOn,pagecentre=FALSE)"]
["  barplot(as.matrix(viaok[idx[1:12],c(\"mn\",\"ma\",\"mc\")]),names.arg=c(\"Normal\",\"Adenoma\",\"Cancer\"),beside=TRUE,main=\"Mean Gene Expression\", legend=viaok[idx[1:12],]$ApprovedSymbol,args.legend = list(x = \"topleft\",cex=1))"]
["  dev.off()"]
["}"]

{"sheet":"D.E.Top-5 in adenoma and cancer","index":4,"n_rows":164,"n_cols":20,"rows_kept":164,"cut":false,"hidden":false,"merged":[[43,18,43,19],[42,12,42,19],[116,12,116,19],[117,18,117,19],[117,14,117,15],[117,16,117,17],[117,12,117,13],[117,10,117,11],[4,12,4,13],[4,14,4,15],[4,16,4,17],[43,12,43,13],[43,14,43,15],[43,10,43,11],[43,16,43,17],[0,0,0,19],[4,18,4,19],[3,12,3,19],[2,0,2,19],[3,4,3,11],[4,8,4,9],[4,10,4,11],[149,0,153,0],[159,0,163,0],[3,2,3,3],[4,2,4,3],[42,2,42,3],[43,2,43,3],[116,2,116,3],[117,2,117,3],[115,0,115,18],[116,4,116,10],[124,0,128,0],[139,0,143,0],[144,0,148,0],[117,4,117,5],[117,6,117,7],[117,8,117,9],[50,0,54,0],[60,0,64,0],[75,0,79,0],[85,0,89,0],[90,0,94,0],[105,0,109,0],[21,0,25,0],[36,0,40,0],[41,0,41,18],[42,4,42,10],[45,0,49,0],[43,4,43,5],[43,6,43,7],[43,8,43,9],[6,0,10,0],[11,0,15,0],[4,4,4,5],[4,6,4,7]],"flags":["formulas_cached_only"]}
["Top-5 ranking genes with fold changes by subpathways. Consensus genes are in green. See Fig. 2 in paper."]
[]
["DDR Pathway"]
[null,null,"COLON",null,"ADENOMA",{"$nulls":7},"CANCER"]
["SUBPATHWAYS","R","INFLAM.",null,"COLON",null,"ADRENAL",null,"PANCREATIC",null,"THYROID",null,"COLON",null,"ADRENAL",null,"PANCREATIC",null,"THYROID"]
[null,null,"Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C."]
["Base Excision Repair",1,null,null,"POLE4",1.05511063474225,"MSH2",1.31147399080818,null,null,"MSH6",1.11718096520105]
[null,2,null,null,"ERCC6",1.05077076420597,"MSH6",1.24771689810325,null,null,"MSH3",1.09014799746286]
[null,3,null,null,"MSH6",1.05016500647627,"MSH3",1.20176766883634,null,null,"PCNA",1.07233894194597]
[null,4,null,null,"MSH3",1.02856097729297,"PARP2",1.17874048495763,null,null,"HMGB2",1.07214453910427]
[null,5,null,null,"MSH2",1.02,"HMGB2",1.14910635362543,null,null,"MSH2",1.06496770942278]
["Fanconi Anemia Pathway",1,null,null,"BRCA2",1.04191147845821,"ATM",1.23612351832302]
[null,2,null,null,"FANCD2",1.03580910134724,"ATR",1.07795366551681]
[null,3,null,null,"FANCC",1.03,"FANCD2",1.0734260795504]
[null,4,null,null,"ATR",1.03255911277111,"ATR",1.0692771749157]
[null,5,null,null,"ATM",1.02409852026927,"ATM",1.05436393740903]
[null,1,null,null,"MUS81",1.07660968040195,"RAD50",1.22311917792207,{"$nulls":6},"RAD52",1.33123377203514,"RPA4",1.26231337069399]
["Homologous",2,null,null,"MRE11A",1.05078189724189,"RAD54B",1.21089013406688,{"$nulls":6},"RAD50",1.22297218549589,"RAD52",1.22805110623085]
[" Recombination",3,null,null,"BRCA2",1.04191147845821,"RAD51C",1.1905981571764,{"$nulls":6},"RPA4",1.21670254037406,"MRE11A",1.18099925468504]
[null,4,null,null,"EME2",1.04152366813252,"RAD52",1.15517418547626,{"$nulls":6},"RAD51L3",1.16757044921556,"MRE11A",1.13576565226862]
[null,5,null,null,"TOP3B",1.03574255179667,"NBN",1.13464732892754,{"$nulls":6},"RAD52",1.16184673642171,"BRCA2",1.13053201293842]
["Mismatch Repair",1,null,null,"MSH6",1.05016500647627,"MSH2",1.31147399080818,{"$nulls":6},"MLH3",1.23946982054361,null,null,"RFC1",1.12252146709581]
[null,2,null,null,"RFC1",1.04553880188278,"RFC3",1.30116363166543,{"$nulls":6},"RPA4",1.21670254037406,null,null,"PRKCG",1.11850393268518]
[null,3,null,null,"RFC3",1.02965102570566,"MSH6",1.24771689810325,{"$nulls":6},"MSH2",1.19786410359605,null,null,"RFC4",1.11275945321751]
[null,4,null,null,"MSH3",1.02856097729297,"MSH3",1.20176766883634,{"$nulls":6},"RFC4",1.17456291729867,null,null,"RFC1",1.10579028564048]
[null,5,null,null,"RFC1",1.02738005450253,"RFC4",1.19937415723,{"$nulls":6},"RFC1",1.17241297243386,null,null,"MSH4",1.10044445022016]
[null,1,null,null,"POLE4",1.05511063474225,"CUL4B",1.31700480428849,{"$nulls":6},"CUL4A",1.32570608210465,null,null,"RFC1",1.12252146709581]
["Nucleotide ",2,null,null,"ERCC6",1.05077076420597,"ERCC8",1.31371766874226,{"$nulls":6},"TP53",1.2255040552903,null,null,"RFC4",1.11275945321751]
["Excision Repair",3,null,null,"RFC1",1.04553880188278,"RFC3",1.30116363166543,{"$nulls":6},"RPA4",1.21670254037406,null,null,"RFC1",1.10579028564048]
[null,4,null,null,"LIG4",1.05511063474225,"CUL4B",1.2157482459804,{"$nulls":6},"ERCC5",1.19697860137405,null,null,"POLD1",1.09627077590131]
[null,5,null,null,"BRCA2",1.04191147845821,"GTF2H1",1.20497201198258,{"$nulls":6},"RFC4",1.17456291729867,null,null,"RFC3",1.09349333085097]
[null,1,{"$nulls":4},"XRCC4",1.29866372739352,"XRCC4",1.67352770060267,"MRE11A",1.10409933198216,null,null,"DCLRE1C",1.25989286346207,null,null,"POLL",1.09085136924529]
["Non-Homologous ",2,{"$nulls":4},"RAD50",1.22311917792207,"LIG4",1.29350331693209,"XRCC4",1.06475860421925,null,null,"RAD50",1.22297218549589,null,null,"FEN1",1.07845926450367]
["end Joining",3,{"$nulls":4},"DCLRE1C",1.1815835192117,"DCLRE1C",1.25848058264936,"RAD50",1.04433568545587,null,null,"DCLRE1C",1.1964468756708,null,null,"POLA1",1.07066683357069]
[null,4,{"$nulls":4},"DCLRE1C",1.16261238999062,"PRKDC",1.22069463804493,"FEN1",1.04174169417443,null,null,"XRCC5",1.17072541933102,null,null,"XRCC4",1.06744184858963]
[null,5,{"$nulls":4},"PRKDC",1.13571182695799,"DCLRE1C",1.21463102637083,"DCLRE1C",1.03547875351242,null,null,"DCLRE1C",1.15494598325312,null,null,"XRCC4",1.05573564082492]
["Double-Strand B. Repair",1,null,null,"BRCA2",1.05078189724189,"XRCC4",1.29866372739352,"XRCC4",1.67352770060267,{"$nulls":4},"RAD52",1.33123377203514,null,null,"NBN",1.15045262089533]
[null,2,null,null,"TP53BP1",1.04191147845821,"ATM",1.23612351832302,"BRCA2",1.34640356563126,null,null,"H2AFX",0.996063288554113,"RAD50",1.22297218549589,null,null,"H2AFX",1.11719985813294]
[null,3,null,null,"LIG4",1.03754609724524,"RAD50",1.22311917792207,"TP53BP1 ",1.29350331693209,null,null,"XRCC6",1.01053149271958,"XRCC5",1.17072541933102,null,null,"RAD51",1.1106957911723]
[null,4,null,null,"MRE11A",1.03225375073626,"RAD52",1.15517418547626,"BRCA2",1.26511635991052,null,null,"XRCC5",1.03754609724524,"RAD52",1.16184673642171,null,null,"H2AFX",1.07780861158056]
[null,5,null,null,"RAD52",1.03023581408436,"PRKDC",1.13571182695799,"PRKDC",1.22069463804493,null,null,"RAD52",1.01203128891094,"XRCC4",1.14266351466173,null,null,"BRCA1",1.07418072986825]
["Apoptosis Pathway"]
[null,null,"COLON",null,"ADENOMA",{"$nulls":7},"CANCER"]
["SUBPATHWAYS","R","INFLAM.",null,"COLON",null,"ADRENAL",null,"PANCREATIC",null,"THYROID",null,"COLON",null,"ADRENAL",null,"PANCREATIC",null,"THYROID"]
[null,null,"Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C."]
["tnfr1 Signaling Pathway",1,{"$nulls":4},"CASP8",1.30390923938799,"BIRC3",1.37562629028875,"CASP2",1.06826044882786]
[null,2,{"$nulls":4},"MAP2K4",1.15210596499822,"CASP3",1.30738125173619,"CASP2",1.06358650634733]
[null,3,{"$nulls":4},"BAG4",1.12786966105729,"CASP2",1.21974004116632,"CASP2",1.06333296365786]
[null,4,{"$nulls":4},"BAG4",1.11019079457819,"MAP2K4",1.19811341824236,"MADD",1.05101064500378]
[null,5,{"$nulls":4},"BAG4",1.1047725754684,"RIPK1",1.11144117859242,"TNF",1.02871677130486]
["tnfr2 Signaling Pathway",1,null,null,"MAP3K14",1.08753844274918,"TANK",1.3001332240046,null,null,"TNFRSF1B",1.17497417807258]
[null,2,null,null,"RIPK1",1.06067757874945,"TNFRSF1B",1.11876234998961,null,null,"TANK",1.10211256537057]
[null,3,null,null,"TNFRSF1B",1.05240846451846,"RIPK1",1.10020681135524,null,null,"TRAF3",1.03735263424549]
[null,4,null,null,"TANK",1.02355835299946,"MAP3K1",1.09431067519757,null,null,"TANK",1.02560857548059]
[null,5,null,null,"MAP3K1",1.02315687188433,"LTA",1.08620968645974,null,null,"MAP3K14",1.01795923641233]
[null,1,{"$nulls":4},"CASP8",1.30390923938799]
["TNF Receptor ",2,{"$nulls":4},"STAT1",1.22508654355127]
["Signaling Pathway",3,{"$nulls":4},"MAP3K7IP2",1.18260252217076]
[null,4,{"$nulls":4},"NSMAF",1.17467078084514]
[null,5,{"$nulls":4},"MAP3K7",1.1493112272733]
["Death Receptor Signalling",1,null,null,"CFLAR",1.06118223429717,null,null,"FAS",1.55308359600487]
[null,2,null,null,"TNFRSF1B",1.06067757874945,null,null,"TNFSF10",1.41243491981861]
[null,3,null,null,"TNFRSF10B",1.05803111844997,null,null,"CFLAR",1.40347094799436]
[null,4,null,null,"FASLG",1.03849489354678,null,null,"FAS",1.37124525525143]
[null,5,null,null,"CASP8",1.03438138024585,null,null,"FAS",1.31220782204769]
[null,1,{"$nulls":8},"CASP6",1.12969535065208]
["Apoptotic Signaling",2,{"$nulls":8},"BCL2",1.12758038900121]
["in Response to ",3,{"$nulls":8},"BAX",1.11327550827558]
["DNA Damage",4,{"$nulls":8},"BCL2L1",1.10886042721581]
[null,5,{"$nulls":8},"BAX",1.10314260136667]
[null,1,{"$nulls":8},"CASP6",1.12969535065208]
["Induction of apoptosis ",2,{"$nulls":8},"TNFSF10",1.12360588590629]
["through dr3 and dr4/5 ",3,{"$nulls":8},"TNFRSF10B",1.06283079729025]
["death receptors",4,{"$nulls":8},"GAS2",1.05870303615533]
[null,5,{"$nulls":8},"LMNA",1.05771877717682]
["Apoptosis - HS",1,"BIRC3",1.10317229089302,null,null,"FAS",1.34226487868508,null,null,"CFLAR",1.20214635537695]
[null,2,"NTRK1",1.09880991668551,null,null,"CFLAR",1.3317944082765,null,null,"AKT2",1.17764254801014]
[null,3,"TNFRSF10D",1.08307552255838,null,null,"PIK3CA",1.31735982702477,null,null,"PRKACB",1.16496179625641]
[null,4,"TNFRSF10B",1.07686362463657,null,null,"TNFSF10",1.31225295032116,null,null,"CASP6",1.12969535065208]
[null,5,"BAX",1.07497216020453,null,null,"PPP3R1",1.30921448264023,null,null,"CFLAR",1.12768412228144]
[null,1,null,null,"NUMA1",1.26438390581946]
["Caspase Cascade ",2,null,null,"APP",1.10682101708345]
["in Apoptosis",3,null,null,"BIRC3",1.09880991668551]
[null,4,null,null,"MAP3K1",1.08753844274918]
[null,5,null,null,"BAX",1.07089648189438]
["Regulation of Apoptosis",1,null,null,"PSMB2",1.07657271759823,"PAK2",1.17463511436262,null,null,"DAPK3",1.20787814639064,null,null,"UNC5A",1.20787527974428,"PSMA3",1.19673478936499,"DAPK3",1.20827927153953]
[null,2,null,null,"PSMC2",1.06194152408119,"PSMC2",1.16835747020351,null,null,"PAK2",1.12378592613169,null,null,"DAPK1",1.16157020314752,"PSMB1",1.19103981077399,"DAPK1",1.11961476526129]
[null,3,null,null,"PSMD7",1.03536100726166,"PSMD11",1.14080203847157,null,null,"DAPK1",1.12067113520064,null,null,"UBC",1.15964644243351,"PSMB7",1.18945553605859,"PSMB8",1.0867407046308]
[null,4,null,null,"PAK2",1.02797631209361,"PSMD12",1.13590720482337,null,null,"PSMF1",1.09933202947509,null,null,"PSME3",1.14305760562362,"UNC5A",1.16397912762959,"DAPK1",1.0842192074076]
[null,5,null,null,"DAPK2",1.02726788509415,"PSMB4",1.1224637534422,null,null,"PSMA2",1.05963925916656,null,null,"PAK2",1.13985234128937,"PAK2",1.14884570475239,"PAK2",1.05833015535798]
["Apoptotic Execution  Ph.",1]
[null,2]
[null,3]
[null,4]
[null,5]
[null,1,{"$nulls":6},"FAS",1.55308359600487]
["Extrinsic Pathway ",2,{"$nulls":6},"TNFSF10",1.41243491981861]
["for Apoptosis",3,{"$nulls":6},"CFLAR",1.40347094799436]
[null,4,{"$nulls":6},"FAS",1.37124525525143]
[null,5,{"$nulls":6},"FAS",1.31220782204769]
[null,1,"SET",1.09955861655169]
["Granzyme A Mediated",2,"HMGB2",1.02842150299811]
[" Apoptosis Pathway",3,"APEX1",1.02697411115538]
[null,4,"ANP32A",1.01941606547631]
[null,5,"HMGB2",1.00892418220379]
["Replicative Senescence",1,"CDK6",1.05260328109429,"CDK6",1.14553178880112,"ATM",1.23612351832302,"RPA4",1.39511463915122,"CCND2",1.21145932318664,"PML",1.13550731643916,"TP53",1.2255040552903,"MDM2",1.64885103828954,"H2AFX",1.17297323417073]
[null,2,"CDC25A",1.04845380081214,"CDC25A",1.12357526782002,"RAD50",1.22311917792207,"BRCA1",1.34640356563126,"CDKN1A",1.19442535698675,"CDK6",1.11355257603767,"RAD50",1.22297218549589,"RPA4",1.26231337069399,"NBN",1.15045262089533]
[null,3,"CDK6",1.03255911277111,"PML",1.10937834442796,"CDK6",1.21290135533493,"BCL2",1.26047217731399,"MDM2",1.16731286702381,"TP53BP1",1.11038766518303,"RPA4",1.21670254037406,"ATR",1.19073521515068,"ATR",1.11719985813294]
[null,4,"CCNE2",1.02409852026927,"CDK6",1.07587656478358,"TP53",1.17379811892825,"CCNE2",1.25545842756704,"CCND2",1.16175059200104,"H2AFX",1.06993764392967,"CDK6",1.20500160286782,"MRE11A",1.18099925468504,"TP53",1.11292497860454]
[null,5,"CDKN1A",1.01906568048688,"CDKN1A",1.06855756365374,"MAPK14",1.1508703188667,"MDM2",1.22624846913084,"MDM2",1.15996474340158,"PML",1.0654081727814,"CCND1",1.20212790499831,"CDKN1A",1.13578318800476,"CCND1",1.11044474012693]
[null,1,{"$nulls":4},"XIAP",1.258789952,null,null,"NEMO",1.13603373904354,null,null,"NRN",1.195170416,"ERC1",1.10898152644303,"NBN",1.15045262089533]
[null,2,{"$nulls":4},"ERC1",1.182602522,null,null,"XIAP",1.11251356089283,null,null,"NEMO",1.166716062,"XIAP",1.10754804451587,"RELA",1.07272622604134]
["NFKB Pathway",3,{"$nulls":4},"NEMO",1.155457711,null,null,"ERC1",1.10409933198216,null,null,"PIAS4",1.162505828,"NR2C2",1.1044602804306,"PIAS4",1.06963387091696]
[null,4,{"$nulls":4},"CHUK",1.146525884,null,null,"CHUK",1.09549248176211,null,null,"XIAP",1.161408309,"NEMO",1.09443437292648,"NFKB1",1.05694128293046]
[null,5,{"$nulls":4},"PIAS4",1.132178425,null,null,"PIAS4",1.06475860421925,null,null,"XIAP",1.158378981,"NBN",1.0913249345834,"NEMO",1.04563741906409]
["Cell Cycle Pathway"]
[null,null,"COLON",null,"ADENOMA",{"$nulls":7},"CANCER"]
["SUBPATHWAYS","R","INFLAM.",null,"COLON",null,"ADRENAL",null,"PANCREATIC",null,"THYROID",null,"COLON",null,"ADRENAL",null,"PANCREATIC",null,"THYROID"]
[null,null,"Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C.","Top-5 genes","Fold C."]
[null,1,{"$nulls":4},"ATM",1.23612351832302,"CDC2",2.01791959201809,{"$nulls":4},"TP53",1.2255040552903]
["Cell Cycle: G1/S",2,{"$nulls":4},"TP53",1.17379811892825,"CDKN2B",1.91441358100733,{"$nulls":4},"TGFB1",1.13837161422761]
["Checkpoints",3,{"$nulls":4},"TP53",1.141056493313,"DHFR",1.36581181368606,{"$nulls":4},"GSK3B",1.12620611071856]
[null,4,{"$nulls":4},"CDKN2A",1.11623022875815,"DHFR",1.29534499412434,{"$nulls":4},"ATM",1.12429435866898]
[null,5,{"$nulls":4},"TGFB1",1.11068265386943,"GSK3B",1.28993024727598,{"$nulls":4},"RB1",1.09011724511557]
["S Phase",1,null,null,"CDC25A",1.12357526782002,null,null,"PSMC2",1.30412530025594,{"$nulls":4},"RFC4",1.22764476074217,null,null,"RFC4",1.23700072125476]
[null,2,null,null,"MCM6",1.09400064741858,null,null,"CCNA2",1.28363695227008,{"$nulls":4},"MCM7",1.21592265240104,null,null,"WEE1",1.17697659635456]
[null,3,null,null,"MYC",1.09025844485626,null,null,"POLE2",1.26138820944327,{"$nulls":4},"MCM5",1.20363711451189,null,null,"WEE1",1.16838409929568]
[null,4,null,null,"CCNE2",1.08840216792453,null,null,"CCNE2",1.25545842756704,{"$nulls":4},"ORC2L",1.20212790499831,null,null,"MYC",1.12252146709581]
[null,5,null,null,"WEE1",1.08186723391312,null,null,"PSMA3",1.24299870307421,{"$nulls":4},"CCND1",1.17456291729867,null,null,"CCNA2",1.11573686794097]
[null,1,{"$nulls":6},"CDC2",2.01791959201809]
["Cyclins and Cell ",2,{"$nulls":6},"CDKN2B",1.91441358100733]
["Cycle Regulation",3,{"$nulls":6},"CCNB1",1.79950391207609]
[null,4,{"$nulls":6},"RBL1",1.28778659172851]
[null,5,{"$nulls":6},"CCNB1",1.24012292808896]
[null,1,{"$nulls":6},"PSMC2",1.30412530025594,"CDKN1A",1.16731286702381,{"$nulls":6},"TP53",1.0867407046308]
["G1/S DNA ",2,{"$nulls":6},"CCNE2",1.25545842756704,"MDM2",1.15996474340158,{"$nulls":6},"PSMB8",1.07852818141225]
["Damage Checkpoints",3,{"$nulls":6},"PSMA3",1.24299870307421,"PSMF1",1.09933202947509,{"$nulls":6},"CDC25A",1.06059997988547]
[null,4,{"$nulls":6},"CHEK1",1.22624846913084,"MDM2",1.08776265374553,{"$nulls":6},"CCNE1",1.05484147128611]
[null,5,{"$nulls":6},"PSMB8",1.22192040766698,"TP53",1.07161628220598,{"$nulls":6},"PSMD9",1.05243633830059]
["G2/M Checkpoints",1,{"$nulls":6},"CDC2",2.01791959201809,"WEE1",1.23184951555709,null,null,"RFC4",1.22764476074217]
[null,2,{"$nulls":6},"CCNB1",1.79950391207609,"RFC4",1.16066571154133,null,null,"MCM7",1.21592265240104]
[null,3,{"$nulls":6},"CDC7",1.53731696832064,"WEE1",1.11264982378368,null,null,"MCM5",1.20363711451189]
[null,4,{"$nulls":6},"MCM10",1.29130461576033,"RFC5",1.07113880226682,null,null,"ORC2L",1.17456291729867]
[null,5,{"$nulls":6},"CCNB2",1.25020686580255,"CDC2",1.06843919132583,null,null,"MCM7",1.16332588213379]
["Mitotic G2-G2/M Phases",1,null,null,"NUMA1",1.26438390581946,null,null,"CDC2",2.01791959201809]
[null,2,null,null,"CDC25A",1.12357526782002,null,null,"CCNB1",1.79950391207609]
[null,3,null,null,"AKAP9",1.1060677424381,null,null,"CCNA2",1.28363695227008]
[null,4,null,null,"WEE1",1.08186723391312,null,null,"CLASP1",1.26863773168129]
[null,5,null,null,"PAFAH1B1",1.0727844801189,null,null,"CEP110",1.250243597063]
["Mitotic M-M/G1 Phases",1,null,null,"CDC7",1.12273804125699,"MAD2L1",1.2478520208009,"CDC7",1.53731696832064,"CLASP1",1.1365870898396,null,null,"RPA4",1.22764476074217,"RPA4",1.26231337069399]
[null,2,null,null,"FBXO5",1.09400064741858,"ORC2L",1.23023413466497,"CENPK",1.46031469964255,"MAD1L1",1.10952613951435,null,null,"MCM7",1.21670254037406,"CDC7",1.23847324680435]
[null,3,null,null,"SMC3",1.07657271759823,"PAFAH1B1",1.22378524837932,"CENPF",1.44907718826609,"PSMF1",1.09933202947509,null,null,"MCM5",1.21592265240104,"DBF4",1.20865333953399]
[null,4,null,null,"PAFAH1B1",1.0727844801189,"GMNN",1.19373707823518,"CENPF",1.44692616392687,"MAD2L1",1.07359896986961,null,null,"ORC2L",1.20363711451189,"PSMA3",1.19673478936499]
[null,5,null,null,"PSMC2",1.06194152408119,"SMC3",1.19262896462338,"MAD2L1",1.41775591442628,"ZWINT",1.0679588252787,null,null,"MCM7",1.18152691531533,"PSMB1",1.19103981077399]
[null,1,{"$nulls":6},"MAD2L1",1.41775591442628]
["Mitotic Spindle",2,{"$nulls":6},"BUB1B",1.38951184263595]
["Checkpoint",3,{"$nulls":6},"ANAPC1",1.3077655002332]
[null,4,{"$nulls":6},"CDC20",1.30159929493908]
[null,5,{"$nulls":6},"UBE2D1",1.20371538514384]
["RB/E2F pathway",1,null,null,"CDC14A",1.18986761277409,null,null,"CDC2",2.01791959201809,"WEE1",1.23184951555709,"EP300",1.05502684293886,"APC",1.22989837595506,"EP300",1.64885103828954,"CREBBP",1.23700072125476]
[null,2,null,null,"CREBBP",1.09955861655169,null,null,"E2F8",1.76164007302068,"CDKN1A",1.16731286702381,"CREBBP",1.04216428819783,"TP53",1.2255040552903,"EED",1.24220663459933,"WEE1",1.17697659635456]
[null,3,null,null,"WEE1",1.08186723391312,null,null,"EED",1.55118838419213,"MDM2",1.15996474340158,"MYT1",1.03046779428468,"EED",1.21386914957049,"APC",1.20613939461532,"WEE1",1.15454962923753]
[null,4,null,null,"TFDP2",1.07102620914913,null,null,"CDC14A",1.3760892107095,"EP300",1.14725533397215,"MYT1",1.02992510602494,"MGA",1.20254667377499,"MDM2",1.20048069466218,"CDKN2B",1.1442374253297]
[null,5,null,null,"EED",1.0693366882715,null,null,"EP300",1.34875376336133,"CCND1",1.14724402444028,"EP300",1.02261787764908,"EED",1.20212790499831,"E2F8",1.18232024586227,"CDKN2B",1.11659433003155]

{"sheet":"D.E. - Top genes in cancer","index":5,"n_rows":172,"n_cols":10,"rows_kept":172,"cut":false,"hidden":false,"merged":[[121,2,121,9],[122,8,122,9],[122,6,122,7],[122,4,122,5],[122,2,122,3],[98,0,102,0],[108,0,113,0],[3,2,3,9],[2,0,2,9],[67,0,71,0],[43,2,43,9],[44,8,44,9],[44,6,44,7],[44,4,44,5],[44,2,44,3],[0,0,0,9],[1,0,1,9],[42,0,42,9],[140,0,144,0],[78,0,82,0],[83,0,87,0],[88,0,92,0],[93,0,97,0],[56,0,60,0],[61,0,66,0],[166,0,171,0],[114,0,119,0],[124,0,128,0],[129,0,134,0],[135,0,139,0],[120,0,120,9],[145,0,149,0],[150,0,155,0],[156,0,160,0],[161,0,165,0],[51,0,55,0],[4,2,4,3],[21,0,25,0],[46,0,50,0],[26,0,30,0],[31,0,35,0],[36,0,40,0],[4,4,4,5],[4,6,4,7],[4,8,4,9],[16,0,20,0],[6,0,10,0],[11,0,15,0]],"flags":["formulas_cached_only"]}
["In gray genes that are upregulated in adenoma (Fig. 3a) and become downregulated in cancer (Fig. 3b). "]
["Genes that remained active in cancer are shown in red (Fig. 3b). "]
["DDR Pathway"]
[null,null,"CANCER"]
["SUBPATHWAYS","R","COLON",null,"ADRENAL",null,"PANCREATIC",null,"THYROID"]
[null,null,"Top-5 genes","Fold Change","Top-5 genes","Fold Change","Top-5 genes","Fold Change","Top-5 genes","Fold Change"]
["Base Excision Repair",1,"MSH6",0.855251796818265,{"$nulls":4},"UNG",0.774091698955087]
[null,2,"MBD4",0.894466272986091,{"$nulls":4},"MBD4",0.848988121165637]
[null,3,"FEN1",0.89489531626423,{"$nulls":4},"TDG",0.852490404409258]
[null,4,"MSH3",0.907594446429669,{"$nulls":4},"MSH3",0.871278762790794]
[null,5,"FEN1",0.907594446429669,{"$nulls":4},"MSH6",0.881261867352753]
["Fanconi Anemia Pathway",1,"FANCD2",0.912968809454116]
[null,2,"BRCA2",0.928928285350217]
[null,3,"FANCA",0.935606174108778]
[null,4,"BRCA2",0.939667389383618]
[null,5,"BRCA1",0.952781255970805]
["Homologous Recombination",1,"SSBP1",0.91375544795304]
[null,2,"RAD51L3",0.911429599175008]
[null,3,"RAD54B",0.905609433196431]
[null,4,"MRE11A",0.8995989553399]
[null,5,"BRCA2",0.881655953460075]
["Mismatch Repair",1,"MSH6",0.855251796818265]
[null,2,"RFC3",0.888210209409323]
[null,3,"MSH2",0.907594446429669]
[null,4,"MSH3",0.917338578253225]
[null,5,"RFC4",0.917733896427713]
["Nucleotide Excision Repair",1,"GTF2H2",0.885011750045444]
[null,2,"RFC3",0.888210209409323]
[null,3,"RAD23B",0.90164993764522]
[null,4,"LIG4",0.917733896427713]
[null,5,"BRCA2",0.922808580581643]
["Non-Homologous  end Joining",1,{"$nulls":4},"XRCC4",0.860425462765886,"PRKDC",0.771641259531809]
[null,2,{"$nulls":4},"FEN1",0.891161494311563,"DCLRE1C",0.93330170511754]
[null,3,{"$nulls":4},"FEN1",0.89351361052677,"RAD50",0.951377184756201]
[null,4,{"$nulls":4},"LIG4",0.894893593981241,"MRE11A",0.969687004146966]
[null,5,{"$nulls":4},"DCLRE1C",0.897063645947639,"XRCC4",0.97504068008444]
["Double-Strand B. Repair",1,"BRCA2",0.905609433196431,null,null,"RAD52",0.847107621512683]
[null,2,"LIG4",0.91375544795304,null,null,"PRKDC",0.860425462765886]
[null,3,"MRE11A",0.924772250250153,null,null,"XRCC4",0.867104338269212]
[null,4,"NBN",0.926005600897325,null,null,"TP53BP1",0.87604965744043]
[null,5,"TP53BP1",0.928995015572983,null,null,"BRCA2",0.897063645947639]
[]
["Apoptosis Pathway"]
[null,null,"CANCER"]
["SUBPATHWAYS","R","COLON",null,"ADRENAL",null,"PANCREATIC",null,"THYROID"]
[null,null,"Top-5 genes","Fold Change","Top-5 genes","Fold Change","Top-5 genes","Fold Change","Top-5 genes","Fold Change"]
["TNFR1 Signaling Pathway",1,null,null,"TRADD",0.897127617777446,"CASP2",0.897396269176672,"MAP2K4",0.850985243211687]
[null,2,null,null,"CASP2",0.901098251722219,"CASP2",0.897683847529576,"BAG4",0.916288783055151]
[null,3,null,null,"CASP8",0.902250153575217,"MAP2K4",0.903641950684303,"TRADD",0.941658028238777]
[null,4,null,null,"BAG4",0.920819135233952,"BIRC3",0.926678355120848,"BIRC3",0.97597337804351]
[null,5,null,null,"MAP2K4",0.921227874921863,"RIPK1",0.933975276197914,"CASP2",0.98117705266426]
["TNFR2 Signaling Pathway",1,"TNFRSF10B",0.955222972276463,"TNFRSF10B",0.952136756163195,null,null,"TNFRSF10B",0.659396837134927]
[null,2,"TANK",0.958602719902766,"LTA",0.95341034349928,null,null,"TANK",0.953430319488906]
[null,3,"RIPK1",0.967987667015618,"TANK",0.963526145499392,null,null,"MAP3K1",0.994020800610171]
[null,4,"TANK",0.984397895067061,"RIPK1",0.98164821165696,null,null,"RIPK1",0.996794757855591]
[null,5,"MAP3K1",1.00054051176165,"MAP3K1",0.988177788243868,null,null,"TRAF3",1.0025332359867]
["TNF Receptor  Signaling Pathway",1,null,null,"SQSTM1",0.836524604345512]
[null,2,null,null,"MAP2K7",0.851849596046429]
[null,3,null,null,"TRADD",0.897127617777446]
[null,4,null,null,"CASP8",0.901331889433407]
[null,5,null,null,"PRKCZ",0.911126729902952]
["Death Receptor Signalling",1,"FADD",0.975402793062478,null,null,"CFLAR",0.828043030168334]
[null,2,"FADD",0.975864997744294,null,null,"FASLG",0.901971184460714]
[null,3,"CFLAR ",0.980182887245608,null,null,"TRAF2",0.903641950684303]
[null,4,"FADD",0.983754281768824,null,null,"TNFSF10",0.912702365189099]
[null,5,"CASP8",0.990398140472969,null,null,"FAS",0.926678355120848]
[null,"A","TNFRSF10B",1.03612936666419]
["Apoptotic Signaling in Response to  DNA Damage",1,{"$nulls":6},"CASP7",0.884527845257714]
[null,2,{"$nulls":6},"BID",0.92153151564865]
[null,3,{"$nulls":6},"BCL2",0.9263517105076851]
[null,4,{"$nulls":6},"BID",0.942396716872872]
[null,5,{"$nulls":6},"BAX",0.957791267637112]
[null,1,{"$nulls":6},"CASP8",0.850985243211687]
["Induction of apoptosis ",2,{"$nulls":6},"CASP7",0.858714221739256]
["through dr3 and dr4/5 ",3,{"$nulls":6},"TNFSF10",0.884527845257714]
["death receptors",4,{"$nulls":6},"DFFB",0.899610786668438]
[null,5,{"$nulls":6},"LMNA",0.900824790291697]
[null,"A",{"$nulls":6},"TNFRSF10B",1.04]
["Apoptosis - HS",1,null,null,"NTRK1",0.827190441150742,null,null,"IRAK3",0.835965684301482]
[null,2,null,null,"IRAK2",0.843401177976429,null,null,"CFLAR",0.839729437431603]
[null,3,null,null,"IRAK1",0.85277229859906,null,null,"MAP3K14",0.848142914304232]
[null,4,null,null,"PPP3CC",0.858201646512002,null,null,"CFLAR",0.850985243211687]
[null,5,null,null,"FAS",0.859757078082811,null,null,"NGF",0.858714221739256]
["Caspase Cascade  in Apoptosis",1,"BAX ",0.809438476063349]
[null,2,"CYCS",0.892690712393142]
[null,3,"DFFB",0.899878311907534]
[null,4,"GAS2",0.911092392412241]
[null,5,"BIRC3",0.924100152261383]
["Regulation of Apoptosis",1,"CASP3",0.911092392412241,"UNC5A",0.719096856787499,null,null,"PSMF1",0.841335110743444]
[null,2,"PSMC2",0.911680057871558,"CASP9",0.873949547561954,null,null,"PSMC6",0.864051109790365]
[null,3,"PSME3",0.914499795478976,"UNC5A",0.877668601073323,null,null,"PSMD12",0.895521656530287]
[null,4,"PAK2",0.924330114706395,"PSMC2",0.891137061388229,null,null,"PAK2",0.897867944905157]
[null,5,"DAPK2",0.931560233295998,"PAK2",0.906887047931845,null,null,"DAPK2",0.898074684049191]
["Apoptotic Execution  Ph.",1]
[null,2]
[null,3]
[null,4]
[null,5]
["Extrinsic Pathway  for Apoptosis",1,{"$nulls":4},"FASLG",0.828043030168334]
[null,2,{"$nulls":4},"CASP10",0.901971184460714]
[null,3,{"$nulls":4},"TRAF2",0.903641950684303]
[null,4,{"$nulls":4},"CFLAR",0.912702365189099]
[null,5,{"$nulls":4},"FAS",0.926678355120848]
[null,1]
["Granzyme A Mediated",2]
[" Apoptosis Pathway",3]
[null,4]
[null,5]
["Replicative Senescence",1,"CHEK1",0.840444934328224,"E2F2",0.858263393717922,"CCND2",0.84757766978624,"RB1",0.695851488393821]
[null,2,"CHEK1",0.858007817405587,"CDK2",0.869958629533558,"PML",0.847871869615327,"MAP2K3",0.780284545831176]
[null,3,"CDC25A",0.911040901743853,"MAPK12",0.869984767650878,"E2F1",0.861308620077166,"MDM2",0.895165202228223]
[null,4,"NBN",0.926005600897325,"CDC45L",0.874395299939741,"BCL2",0.867104338269212,"CCND1",0.920091178628844]
[null,5,"CDK2",0.92803166354254,"E2F1",0.876466892671453,"MDM2",0.87604965744043,"MAP2K3",0.92153151564865]
[null,"A","CDKN1A",1,{"$nulls":4},"CDKN1A",0.998151326010522]
["NFKB Pathway",1,null,null,"ERC1",0.893625288,null,null,"UBE2N",0.835965684301482]
[null,2,null,null,"UBE2N",0.907965559,null,null,"BIRC2",0.841130423951465]
[null,3,null,null,"NBN",0.922768708,null,null,"MAP3K7IP2",0.848142914304232]
[null,4,null,null,"RELA",0.931544052,null,null,"UBE2N",0.927943404783959]
[null,5,null,null,"ERC1",0.936850799,null,null,"CHUK",0.930540542700347]
[null,"A",null,null,"NEMO",0.96,null,null," NEMO",1.01]
["Cell cycle Pathway"]
[null,null,"CANCER"]
["SUBPATHWAYS","R","COLON",null,"ADRENAL",null,"PANCREATIC",null,"THYROID"]
[null,null,"Top-5 genes","Fold Change","Top-5 genes","Fold Change","Top-5 genes","Fold Change","Top-5 genes","Fold Change"]
["Cell Cycle: G1/S Checkpoints",1]
[null,2]
[null,3]
[null,4]
[null,5]
["S Phase",1,"CDC6",0.834934230616698]
[null,2,"RFC3",0.888210209409323]
[null,3,"CCNA2",0.889750184876553]
[null,4,"FEN1",0.89489531626423]
[null,5,"CDC6",0.89598868297071]
[null,"A","WEE1",1.02]
["Cyclins and Cell  Cycle Regulation",1]
[null,2]
[null,3]
[null,4]
[null,5]
["G1/S DNA Damage Checkpoints",1]
[null,2]
[null,3]
[null,4]
[null,5]
["G2/M Checkpoints",1,{"$nulls":4},"MCM5",0.867104338269212]
[null,2,{"$nulls":4},"MCM4",0.875442701970689]
[null,3,{"$nulls":4},"MCM2",0.904680745175773]
[null,4,{"$nulls":4},"CDC6",0.907719858329399]
[null,5,{"$nulls":4},"CDC7",0.908578666901851]
["Mitotic G2-G2/M Phases",1,"CCNB1",0.850920126029298]
[null,2,"CDC2",0.861894280815808]
[null,3,"CCNB1",0.884441029673557]
[null,4,"CCNA2",0.889750184876553]
[null,5,"CDC2",0.890291946810593]
[null,"A","WEE1",1.02]
["Mitotic M-M/G1 Phases",1,"CDC6",0.834934230616698,"BIRC5",0.824494208869268]
[null,2,"MCM10",0.840087712172992,"FBXO5",0.846734200901649]
[null,3,"BUB1B",0.867941777158119,"POLE",0.855803218199039]
[null,4,"CENPK",0.870392801517457,"E2F2",0.869984767650878]
[null,5,"CDC20",0.871848377903848,"CDK2",0.876466892671453]
["Mitotic Spindle Checkpoint",1]
[null,2]
[null,3]
[null,4]
[null,5]
["RB/E2F pathway",1,"CHEK1",0.840444934328224,{"$nulls":4},"RB1",0.695851488393821]
[null,2,"CHEK1",0.858007817405587,{"$nulls":4},"RYBP",0.780284545831176]
[null,3,"CDC2",0.861894280815808,{"$nulls":4},"EP300",0.886927231885772]
[null,4,"CDC20",0.871848377903848,{"$nulls":4},"APC",0.895930889059562]
[null,5,"CCNB1",0.884441029673557,{"$nulls":4},"EP300",0.898599899990271]
[null,"A","WEE1",1.01797504022867,{"$nulls":4},"WEE1",1.05]