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=Layer specific MHBs with hyper or hypo-MHL= == motivation== * group tissues of same gem layer * identify layder specific MHBs with hyper/hypo MHL == Layer specific hyper-MHL regions== *In total we identified 114 ectoderm-specific MHBs (99 hyper- and 15 hypo-methylated), 75 endoderm specific MHBs (58 hyper and 17 hypo-methylated) and 31 mesoderm specific MHBs (9 hyper and 22 hypo-methylated) (see Methods, Supplementary Table 3). * Figure saved in laptop: C:\Users\shicheng\Dropbox\Project\methylation\monod\analysis\layer_specfic_mhl * Raw data saved in Genome-miner: /home/shg047/monod/dec Rbedtools<-function(functionstring="intersectBed",bed1,bed2,opt.string=""){ #create temp files a.file=tempfile() b.file=tempfile() out =tempfile() options(scipen =99) # not to use scientific notation when writing out #write bed formatted dataframes to tempfile write.table(bed1,file=a.file,quote=F,sep="\t",col.names=F,row.names=F) write.table(bed2,file=b.file,quote=F,sep="\t",col.names=F,row.names=F) # create the command string and call the command using system() command=paste(functionstring,"-a",a.file,"-b",b.file,opt.string,">",out,sep=" ") cat(command,"\n") try(system(command)) res=read.table(out,header=F) unlink(a.file);unlink(b.file);unlink(out) return(res) } cor2bed<-function(cor){ a<-unlist(lapply(strsplit(as.character(cor),split=c(":")),function(x) strsplit(x,"-"))) bed<-matrix(a,ncol=3,byrow=T) return(data.frame(bed)) } setwd("C:\\Users\\shicheng\\Dropbox\\Project\\methylation\\monod\\analysis\\layer_specfic_mhl") /home/shg047/monod/dec/Table.GSI.layer.mhl.WGBS.Remove.H1.WBC.rlt.txt data=read.table("/home/shg047/monod/dec/Table.GSI.layer.mhl.WGBS.Remove.H1.WBC.rlt.txt",head=T,sep="\t",as.is=T) head(data) newdata=subset(data,GSI>0.6) table(subset[,2]) mesoderm<-subset(newdata,group=="Mesoderm") ectoderm<-subset(newdata,group=="Ectoderm") endoderm<-subset(newdata,group=="Endoderm") mesodermBed<-cor2bed(mesoderm[,1]) ectodermBed<-cor2bed(ectoderm[,1]) endodermBed<-cor2bed(endoderm[,1]) # change to laptop to plot histgram setwd("C:\\Users\\shicheng\\Dropbox\\Project\\methylation\\monod\\analysis\\layer_specfic_mhl") data=read.table("Table.GSI.layer.mhl.WGBS.Remove.H1.WBC.rlt.txt",head=T,sep="\t",as.is=T) pdf("hist.layer.specfic.pdf") hist(data[,3],breaks=30,col="green",ylim=c(0,4000),xlab="Layer Specfic Index",main="") dev.off() Rbedtools(functionstring="intersectBed",bed1=mesodermBed,bed2=ectodermBed,opt.string="-wa -u") table<-c(99,66,9) names(table)<-c("Ectoderm","Endoderm","Mesoderm") barplot(table,ylim=c(0,100),col="green") * Layer specific MHBs with hyper-MHL Ectoderm Endoderm Mesoderm 99 66 9 {|style="font-size:80%;" |align="center" style="background:#f0f0f0;"|''' region''' |align="center" style="background:#f0f0f0;"|''' group''' |align="center" style="background:#f0f0f0;"|''' GSI''' |- | chr8:29387092-29387216||Ectoderm||0.659537333117352 |- | chr19:39898750-39898769||Ectoderm||0.622260349526761 |- | chr11:120095770-120095841||Ectoderm||0.638436015070805 |- | chr8:143298766-143298852||Ectoderm||0.629089907645855 |- | chr16:21657412-21657574||Ectoderm||0.6376721097517 |- | chr5:92934330-92934406||Ectoderm||0.667334656563231 |- | chr3:43811289-43811331||Ectoderm||0.658785740481031 |- | chr17:8601976-8601988||Ectoderm||0.602106513421994 |- | chr10:121030613-121030661||Ectoderm||0.620355461223933 |- | chr1:193377965-193378092||Ectoderm||0.612384341440121 |- | chr18:13138062-13138194||Ectoderm||0.630293124544825 |- | chr11:128065158-128065181||Ectoderm||0.615776035999425 |- | chr7:115995198-115995218||Ectoderm||0.639634173881391 |- | chr2:3583886-3583967||Ectoderm||0.629371815688128 |- | chr21:24503682-24503775||Ectoderm||0.60393446974352 |- | chr8:42750431-42750654||Ectoderm||0.609058674400317 |- | chr1:22259946-22260017||Ectoderm||0.600124624290291 |- | chr5:106878574-106878620||Ectoderm||0.609389311058491 |- | chr10:123496262-123496391||Ectoderm||0.633479349721013 |- | chr9:97713223-97713340||Ectoderm||0.602639172712739 |- | chr6:43670518-43670599||Ectoderm||0.616096733986403 |- | chr11:36706919-36707044||Ectoderm||0.639962708993761 |- | chr15:42187197-42187218||Ectoderm||0.607623926207222 |- | chr2:65804207-65804281||Ectoderm||0.603236104868574 |- | chr17:77766959-77766979||Ectoderm||0.66624153932879 |- | chr1:159893108-159893168||Ectoderm||0.671409324490059 |- | chr2:121495455-121495544||Ectoderm||0.616705504439262 |- | chr8:19522859-19522941||Ectoderm||0.61492324445635 |- | chr19:38886666-38886702||Ectoderm||0.670488181288092 |- | chr1:41849182-41849197||Ectoderm||0.601497796230824 |- | chr19:38886138-38886153||Ectoderm||0.60215755360785 |- | chr11:110065132-110065260||Ectoderm||0.620350268299807 |- | chr18:28827952-28828043||Ectoderm||0.62733392232416 |- | chr2:110438251-110438428||Ectoderm||0.609815651189271 |- | chr11:74854298-74854413||Ectoderm||0.604758661736277 |- | chr20:43966567-43966613||Ectoderm||0.633100005220329 |- | chr2:85811833-85811846||Ectoderm||0.603742595694347 |- | chr7:101961892-101961907||Ectoderm||0.636479562937856 |- | chr22:19710901-19710936||Ectoderm||0.643860942397404 |- | chr17:76732402-76732485||Ectoderm||0.630309428917436 |- | chr16:88837350-88837417||Ectoderm||0.639956789529288 |- | chr20:49262297-49262329||Ectoderm||0.62648816520905 |- | chr1:186181479-186181655||Ectoderm||0.605638208915313 |- | chr8:134203271-134203327||Ectoderm||0.620493153208632 |- | chr5:169894194-169894243||Ectoderm||0.633726208035661 |- | chr5:150403465-150403482||Ectoderm||0.62441239036749 |- | chr9:137220495-137220592||Ectoderm||0.600899351123174 |- | chr2:74209501-74209580||Ectoderm||0.602032376155113 |- | chr20:5059205-5059233||Ectoderm||0.612938330332136 |- | chr1:227545247-227545308||Ectoderm||0.609135849889118 |- | chr7:33080614-33080718||Ectoderm||0.639600512160286 |- | chr1:59362446-59362543||Ectoderm||0.619376367184664 |- | chr2:203037243-203037337||Ectoderm||0.625115647207567 |- | chr17:77767155-77767186||Ectoderm||0.638533123496661 |- | chr7:43214618-43214840||Ectoderm||0.600723642889573 |- | chr2:71644560-71644595||Ectoderm||0.641067698816342 |- | chr7:139529310-139529349||Ectoderm||0.6134098285564 |- | chr1:196946446-196946570||Ectoderm||0.610806427586173 |- | chr2:42277283-42277335||Ectoderm||0.628058759527649 |- | chr11:123016107-123016154||Ectoderm||0.657923031208003 |- | chr1:229978819-229978864||Ectoderm||0.623894630744394 |- | chr17:57078908-57079003||Ectoderm||0.610926283216838 |- | chr7:22617356-22617407||Ectoderm||0.667929987625616 |- | chr7:2757237-2757316||Ectoderm||0.601252252195626 |- | chr3:36949925-36949965||Ectoderm||0.662948818910667 |- | chr1:59361425-59361492||Ectoderm||0.658198739198946 |- | chr21:40138947-40139045||Ectoderm||0.641545688027849 |- | chr22:33018091-33018133||Ectoderm||0.605395609371496 |- | chr10:45916330-45916353||Ectoderm||0.627360449725662 |- | chr6:154975205-154975246||Ectoderm||0.607656376219889 |- | chr21:34659414-34659513||Ectoderm||0.614947673577016 |- | chr12:113065670-113065803||Ectoderm||0.637109038086428 |- | chr11:61456495-61456567||Ectoderm||0.603736020447996 |- | chr1:204592540-204592575||Ectoderm||0.600751451839705 |- | chr22:38614662-38614758||Ectoderm||0.65680933946711 |- | chr17:76588327-76588445||Ectoderm||0.655514821551318 |- | chr16:86417535-86417723||Ectoderm||0.621362797865302 |- | chr6:159128335-159128360||Ectoderm||0.648877652085264 |- | chr3:167073066-167073152||Ectoderm||0.648045424921539 |- | chr3:186928712-186928778||Ectoderm||0.610146996868578 |- | chr11:57089649-57089743||Ectoderm||0.62677395784954 |- | chr6:111239079-111239184||Ectoderm||0.63037773416189 |- | chr17:48764127-48764188||Ectoderm||0.60627221893251 |- | chr6:168197479-168197510||Ectoderm||0.632032999449708 |- | chr15:74671324-74671459||Ectoderm||0.623154091775709 |- | chr19:58868085-58868120||Ectoderm||0.674814055759394 |- | chr4:153878727-153878844||Ectoderm||0.62419394200263 |- | chr3:172280812-172280854||Ectoderm||0.625528145281659 |- | chr3:122640840-122640863||Ectoderm||0.606059008480575 |- | chr1:8064972-8064983||Ectoderm||0.644939000855723 |- | chr12:248974-249014||Ectoderm||0.657233142275506 |- | chr19:16272368-16272434||Ectoderm||0.610474524921455 |- | chr5:132444216-132444275||Ectoderm||0.602807461907881 |- | chr15:31890779-31891030||Ectoderm||0.603133103058883 |- | chr21:45579708-45579771||Ectoderm||0.612035579928314 |- | chr22:24906975-24907189||Ectoderm||0.604317977687824 |- | chr21:45304017-45304067||Ectoderm||0.615161807537595 |- | chr17:76732735-76732773||Ectoderm||0.627406271009881 |- | chr20:21250244-21250339||Ectoderm||0.607049177788986 |- | chr17:2119276-2119367||Endoderm||0.621555865969221 |- | chr1:1957051-1957084||Endoderm||0.602650908155007 |- | chr9:35689643-35689690||Endoderm||0.619387701280056 |- | chr2:47241811-47241842||Endoderm||0.662829312044627 |- | chr5:172305920-172305935||Endoderm||0.670739265276362 |- | chr14:38080580-38080592||Endoderm||0.639966474713107 |- | chr1:230476437-230476574||Endoderm||0.635030322574557 |- | chr10:104575592-104575618||Endoderm||0.609149408140753 |- | chr8:12957933-12957984||Endoderm||0.643490818086236 |- | chr5:151043109-151043181||Endoderm||0.680177807411657 |- | chr4:7632491-7632709||Endoderm||0.652423230457514 |- | chr19:3670199-3670225||Endoderm||0.634998241133357 |- | chr7:114584954-114585002||Endoderm||0.603616478692203 |- | chr1:234669276-234669303||Endoderm||0.616809574818785 |- | chr16:22229894-22229955||Endoderm||0.607629291159365 |- | chr10:6216405-6216443||Endoderm||0.602971624717696 |- | chr9:124615379-124615452||Endoderm||0.633955823125635 |- | chr2:37875819-37875959||Endoderm||0.602628500656313 |- | chr2:64242660-64242800||Endoderm||0.60726399310844 |- | chr2:242101288-242101347||Endoderm||0.608076333824482 |- | chr16:1560025-1560087||Endoderm||0.651972214196267 |- | chr11:118081886-118081999||Endoderm||0.6029309710898 |- | chr6:157372211-157372306||Endoderm||0.634278618167255 |- | chr11:65683490-65683558||Endoderm||0.636307514242888 |- | chr18:46316989-46317041||Endoderm||0.624166723941027 |- | chr16:10832062-10832121||Endoderm||0.611440520083738 |- | chr8:1811724-1811734||Endoderm||0.604615438333278 |- | chr22:44759564-44759570||Endoderm||0.610192616512951 |- | chr11:107906691-107906721||Endoderm||0.605751844696818 |- | chr2:239358562-239358706||Endoderm||0.614617410007429 |- | chr1:25062843-25062863||Endoderm||0.670823332436485 |- | chr4:37624974-37625026||Endoderm||0.6544427274209 |- | chr19:36642990-36643069||Endoderm||0.656605450961024 |- | chr12:6664139-6664180||Endoderm||0.669123041535702 |- | chr11:44161686-44161822||Endoderm||0.628887015251611 |- | chr7:459050-459072||Endoderm||0.60012029687524 |- | chr19:39154668-39154690||Endoderm||0.663027710309978 |- | chr17:66511557-66511576||Endoderm||0.631028220970854 |- | chr11:47629283-47629316||Endoderm||0.634080728472571 |- | chr22:34271616-34271645||Endoderm||0.615941002445972 |- | chr1:225954691-225954718||Endoderm||0.601078618642703 |- | chr11:46732432-46732450||Endoderm||0.632603084148886 |- | chr4:151504919-151504983||Endoderm||0.621077562503555 |- | chr11:24086083-24086150||Endoderm||0.608691231029366 |- | chr22:18335966-18336049||Endoderm||0.670754545443272 |- | chr19:18761285-18761327||Endoderm||0.68028737010478 |- | chr5:54887639-54887649||Endoderm||0.652970324942108 |- | chr9:93682361-93682514||Endoderm||0.665920831412597 |- | chr3:170893533-170893551||Endoderm||0.603621933335352 |- | chr3:171024840-171024914||Endoderm||0.636779220273703 |- | chr14:59894932-59895017||Endoderm||0.61228529088177 |- | chr2:1656976-1657034||Endoderm||0.618587759655055 |- | chr16:69961433-69961448||Endoderm||0.631835214629571 |- | chr14:102394447-102394465||Endoderm||0.612365707941321 |- | chr7:6202081-6202133||Endoderm||0.611591150947358 |- | chr19:38664210-38664243||Endoderm||0.602726833114876 |- | chr1:10292194-10292416||Endoderm||0.653640769186138 |- | chr20:19357121-19357136||Endoderm||0.654714700397522 |- | chr2:204553596-204553702||Endoderm||0.601402898925884 |- | chr6:157469645-157469672||Endoderm||0.6380499171651 |- | chr10:115386647-115386737||Endoderm||0.622056663225908 |- | chr2:240234683-240234705||Endoderm||0.612158498128861 |- | chr19:15514987-15514998||Endoderm||0.601666018050405 |- | chr2:109196275-109196451||Endoderm||0.634236535885808 |- | chr12:109240568-109240631||Endoderm||0.614972599326848 |- | chr13:42188452-42188507||Endoderm||0.604875957545443 |- | chr16:85394306-85394334||Mesoderm||0.603027122263449 |- | chr14:34493536-34493559||Mesoderm||0.661457016899424 |- | chr17:79322621-79322654||Mesoderm||0.609437589321225 |- | chr11:655465-655517||Mesoderm||0.638631266023567 |- | chr9:4664295-4664543||Mesoderm||0.622455538468081 |- | chr11:117684083-117684169||Mesoderm||0.614193089173044 |- | chr17:80847496-80847545||Mesoderm||0.614992470215796 |- | chr5:158879531-158879581||Mesoderm||0.631390177181746 |- | chr11:34847402-34847459||Mesoderm||0.657593838020926 |- |} == Layer specific hypo-MHL regions (LSMHB)== * code in Genome-miner library("impute") RawNARemove<-function(data,missratio=0.3){ threshold<-(missratio)*dim(data)[2] NaRaw<-which(apply(data,1,function(x) sum(is.na(x))>threshold)) zero<-which(apply(data,1,function(x) all(x==0))==T) NaRAW<-c(NaRaw,zero) if(length(NaRAW)>0){ dat<-data[-NaRAW,] }else{ dat<-data; } dat } ################################################################################################################### setwd("/home/shg047/monod/dec") infile="WGBS_methHap_load_matrix_20Oct2015.txt"; file1<-read.table(infile,head=T,sep="\t",row.names=1,as.is=T,check.names=F) # miss value detection and imputation library("impute") f2<-RawNARemove(file1,missratio=0.3) f2<-impute.knn(data.matrix(f2))$data colnames(f2) library("preprocessCore") f2.t1<-normalize.quantiles(f2[,13:58]) library("sva") batch=c(rep(1,10),rep(2,36)) f2.t2<-ComBat(f2.t1, batch, mod=NULL, par.prior = TRUE,prior.plots = FALSE) f2[,13:58]<-f2.t2 # re-assign colnames colnames(f2) colnames(f2)<-gsub("_","-",colnames(f2)) colname2<-unlist(lapply(colnames(f2),function(x) unlist(strsplit(x,"[.]"))[1])) colname2 colnames(f2)<-colname2 # be sure all the sample information has been stored in the following database saminfo2<-read.table("/home/shg047/monod/phase2/newsaminfo.txt",head=T,sep="\t",as.is=T) saminfo2<-saminfo2[match(colname2,saminfo2[,1]),] saminfo2 colnames(f2)<-saminfo2[,2] saminfo3<-read.table("/home/shg047/monod/saminfo/tissue2Layer.txt",head=T,sep="\t",as.is=T) f2<-f2[,saminfo2[,2] %in% saminfo3[,1]] fn<-f2 colnames(fn)<-saminfo3[match(colnames(fn),saminfo3[,1]),2] group=names(table(colnames(fn))) index=colnames(fn) gsi<-c() gmaxgroup<-c() pvalue=apply(fn,1,function(x) summary(aov(x~index))[[1]][["Pr(>F)"]][1]) # R list will not be correctly shown in wiki, you can see raw script in edit mode pvalue=apply(fn,1,function(x) summary(aov(x~index))[[1]][[5]][1]) # R list will not be correctly shown in wiki, you can see raw script in edit mode SigDiffMHBANOVA<-fn[match(names(which(pvalue<9.223561e-07)),rownames(fn)),] save(SigDiffMHBANOVA,file="SigDiffMHBANOVA.RData") setwd("C:\\Users\\shicheng\\Dropbox\\Project\\methylation\\monod\\analysis\\layer_specfic_mhl\\anova") library("gplots") load("SigDiffMHBANOVA.RData") SigDiffMHBANOVA[SigDiffMHBANOVA<0]<-0 SigDiffMHBANOVA[SigDiffMHBANOVA>1]<-1 SigDiffMHBANOVA<-SigDiffMHBANOVA[,order(colnames(SigDiffMHBANOVA))] pdf("Figure.supervised.layer.mhl.single.cpg.heatmap.analysis.combat.quantile.pdf") col=colorRampPalette(c("yellow", "blue"))(20) rlt<-heatmap.2(data.matrix(SigDiffMHBANOVA),col=col,trace="none",density.info="none",Colv=T,Rowv=T,key=T,keysize=1,cexCol=0.65,cexRow=0.15) dev.off() * Layer specific MHBs with hypo-MHL # Endoderm specific MHB with hypo-MHL chr11:16023703β16023847 chr8:131774761β131774884 chr7:100540088β100540103 chr5:10746894β10747078 chr14:69095543β69095569 chr1:120333406β120333474 chr4:185071507β185071556 chr15:63682373β63682439 chr6:136869788β136869917 chr15:69854565β69854745 chr2:235372763β235372775 chr7:150074899β150075088 chr11:86716322β86716463 chr10:125866028β125866205 chr20:51697944β51698112 chr11:45670341β45670390 chr13:107772692β107772845 # Mesoderm specific MHB with hypo-MHL chr2:227555394β227555409 chr14:38091850β38091925 chr14:38080503β38080551 chr7:99984750β99984849 chr4:55650506β55650562 chr10:13726663β13726680 chr2:204553596β204553702 chr14:38080580β38080592 chr9:137296113β137296129 chr12:6664139β6664180 chr5:151043109β151043181 chr19:39154699β39154740 chr6:157469645β157469672 chr19:36642990β36643069 chr11:68695417β68695433 chr19:39154668β39154690 chr3:114343145β114343262 chr2:109196275β109196451 chr8:61764645β61764654 chr4:140737662β140737678 chr7:116409578β116409798 chr2:30574091β30574117 # Ectoderm specific MHB with hypo-MHL chr20:32010750β32010885 chr4:56238469β56238664 chr12:15759107β15759119 chr2:27268131β27268232 chr15:43812034β43812191 chr2:118688440β118688576 chr7:141359663β141359879 chr8:9954912β9955067 chr9:92683370β92683559 chr2:201964657β201964684 chr1:93623462β93623507 chr3:142199628β142199667 chr5:118285675β118285700 chr8:95745542β95745573 chr6:107096030β107096062 *TFBS for i in `ls /home/shg047/db/hg19/encode/encode.*.hg19.bed` do bedtools window -w 100 -a endo.mhb.hypo.bed -b $i >> endo.mhb.hypo.tf bedtools window -w 100 -a meso.mhb.hypo.bed -b $i >> meso.mhb.hypo.tf bedtools window -w 100 -a ecto.mhb.hypo.bed -b $i >> ecto.mhb.hypo.tf done cat endo.mhb.hypo.tf | awk '{print $4}' | sort -u > endo.mhb.hypo.uni.tf cat meso.mhb.hypo.tf | awk '{print $4}' | sort -u > meso.mhb.hypo.uni.tf cat ecto.mhb.hypo.tf | awk '{print $4}' | sort -u > ecto.mhb.hypo.uni.tf * File Address in Genome-miner /home/shg047/monod/layer/endo.mhb.hypo.bed /home/shg047/monod/layer/meso.mhb.hypo.bed /home/shg047/monod/layer/ecto.mhb.hypo.bed *Venn graph * Gene Ontolgoy * Endoderm {|style="font-size:80%;" |align="center" style="background:#f0f0f0;"|''' Category''' |align="center" style="background:#f0f0f0;"|''' Term''' |align="center" style="background:#f0f0f0;"|''' Count''' |align="center" style="background:#f0f0f0;"|''' %''' |align="center" style="background:#f0f0f0;"|''' PValue''' |align="center" style="background:#f0f0f0;"|''' Fold Enrichment''' |align="center" style="background:#f0f0f0;"|''' FDR''' |- | GOTERM_MF_FAT||GO:0003700~transcription factor activity||26||86.66666667||1.02E-24||11.54044444||1.08E-21 |- | SP_PIR_KEYWORDS||dna-binding||27||90||1.08E-23||9.267398287||1.06E-20 |- | SP_PIR_KEYWORDS||transcription regulation||27||90||8.77E-23||8.544669299||8.59E-20 |- | SP_PIR_KEYWORDS||Transcription||27||90||1.55E-22||8.359005311||1.51E-19 |- | GOTERM_MF_FAT||GO:0030528~transcription regulator activity||27||90||1.10E-21||7.72797619||1.16E-18 |- | GOTERM_MF_FAT||GO:0003677~DNA binding||29||96.66666667||2.73E-20||5.384055484||2.88E-17 |- | SP_PIR_KEYWORDS||nucleus||30||100||1.12E-19||4.491010974||1.10E-16 |- | GOTERM_BP_FAT||GO:0006350~transcription||27||90||1.82E-18||5.794954783||2.67E-15 |- | GOTERM_BP_FAT||GO:0045449~regulation of transcription||28||93.33333333||1.10E-17||4.854338075||1.62E-14 |- | GOTERM_MF_FAT||GO:0043565~sequence-specific DNA binding||18||60||5.83E-16||12.83327842||5.88E-13 |- | GOTERM_BP_FAT||GO:0006355~regulation of transcription, DNA-dependent||24||80||9.18E-16||6.104004512||1.31E-12 |- | GOTERM_BP_FAT||GO:0051252~regulation of RNA metabolic process||24||80||1.62E-15||5.969332598||2.45E-12 |- | SP_PIR_KEYWORDS||activator||13||43.33333333||4.59E-12||16.02916667||4.50E-09 |- | SP_PIR_KEYWORDS||DNA binding||11||36.66666667||3.88E-11||20.74362745||3.80E-08 |- | GOTERM_BP_FAT||GO:0006357~regulation of transcription from RNA polymerase II promoter||14||46.66666667||8.55E-10||8.683723063||1.26E-06 |- | GOTERM_CC_FAT||GO:0031981~nuclear lumen||13||43.33333333||5.12E-09||6.741014199||5.27E-06 |- | GOTERM_BP_FAT||GO:0010628~positive regulation of gene expression||12||40||1.43E-08||9.313597246||2.10E-05 |- | GOTERM_MF_FAT||GO:0003702~RNA polymerase II transcription factor activity||9||30||4.24E-08||15.96270492||4.47E-05 |- | GOTERM_CC_FAT||GO:0070013~intracellular organelle lumen||13||43.33333333||5.40E-08||5.494362332||5.55E-05 |- | GOTERM_CC_FAT||GO:0043233~organelle lumen||13||43.33333333||7.00E-08||5.370588235||7.20E-05 |- | GOTERM_MF_FAT||GO:0008134~transcription factor binding||11||36.66666667||8.65E-08||9.279597141||9.12E-05 |- | GOTERM_CC_FAT||GO:0031974~membrane-enclosed lumen||13||43.33333333||8.76E-08||5.266417343||9.01E-05 |- | GOTERM_BP_FAT||GO:0045941~positive regulation of transcription||11||36.66666667||1.43E-07||8.794799054||2.11E-04 |- | GOTERM_BP_FAT||GO:0045935~positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process||11||36.66666667||3.67E-07||7.949145299||5.39E-04 |- | GOTERM_BP_FAT||GO:0045893~positive regulation of transcription, DNA-dependent||10||33.33333333||4.17E-07||9.453529001||6.13E-04 |- | GOTERM_BP_FAT||GO:0051254~positive regulation of RNA metabolic process||10||33.33333333||4.47E-07||9.374913375||6.58E-04 |- | GOTERM_BP_FAT||GO:0051173~positive regulation of nitrogen compound metabolic process||11||36.66666667||4.91E-07||7.702277433||7.21E-04 |- | GOTERM_BP_FAT||GO:0010557~positive regulation of macromolecule biosynthetic process||11||36.66666667||5.65E-07||7.584505607||8.31E-04 |- | GOTERM_BP_FAT||GO:0010604~positive regulation of macromolecule metabolic process||12||40||7.44E-07||6.31411902||0.001094283 |- | GOTERM_BP_FAT||GO:0045944~positive regulation of transcription from RNA polymerase II promoter||9||30||7.69E-07||10.93908356||0.001130801 |- | GOTERM_BP_FAT||GO:0031328~positive regulation of cellular biosynthetic process||11||36.66666667||8.65E-07||7.241265207||0.001271592 |- | GOTERM_BP_FAT||GO:0009891~positive regulation of biosynthetic process||11||36.66666667||9.87E-07||7.137074341||0.001451883 |- | GOTERM_BP_FAT||GO:0010551~regulation of specific transcription from RNA polymerase II promoter||6||20||1.51E-06||28.78297872||0.002226717 |- | GOTERM_MF_FAT||GO:0046983~protein dimerization activity||10||33.33333333||1.71E-06||7.984624846||0.001801204 |- | INTERPRO||IPR004827:Basic-leucine zipper (bZIP) transcription factor||5||16.66666667||2.04E-06||52.38679245||0.002102847 |- | GOTERM_MF_FAT||GO:0016563~transcription activator activity||9||30||2.21E-06||9.499756098||0.002335511 |- | UP_SEQ_FEATURE||DNA-binding region:Basic motif||6||20||4.02E-06||23.74285714||0.004570435 |- | SMART||SM00338:BRLZ||5||16.66666667||8.44E-06||35.68789308||0.006326719 |- | GOTERM_BP_FAT||GO:0032583~regulation of gene-specific transcription||6||20||8.68E-06||20.19104478||0.0127626 |- | UP_SEQ_FEATURE||domain:Leucine-zipper||5||16.66666667||2.21E-05||28.95909091||0.025103574 |- | GOTERM_BP_FAT||GO:0006351~transcription, DNA-dependent||7||23.33333333||3.00E-05||10.81004566||0.044147909 |- | GOTERM_BP_FAT||GO:0032774~RNA biosynthetic process||7||23.33333333||3.24E-05||10.66396396||0.047654411 |- | SP_PIR_KEYWORDS||repressor||7||23.33333333||3.95E-05||10.31762452||0.038665521 |- | UP_SEQ_FEATURE||zinc finger region:NR C4-type||4||13.33333333||4.27E-05||56.63111111||0.048544142 |- | UP_SEQ_FEATURE||DNA-binding region:Nuclear receptor||4||13.33333333||4.27E-05||56.63111111||0.048544142 |- |} *Mesoderm {|style="font-size:80%;" |align="center" style="background:#f0f0f0;"|''' Category''' |align="center" style="background:#f0f0f0;"|''' Term''' |align="center" style="background:#f0f0f0;"|''' Count''' |align="center" style="background:#f0f0f0;"|''' %''' |align="center" style="background:#f0f0f0;"|''' PValue''' |align="center" style="background:#f0f0f0;"|''' Fold Enrichment''' |align="center" style="background:#f0f0f0;"|''' FDR''' |- | SP_PIR_KEYWORDS||transcription regulation||12||92.30769231||1.87E-10||8.763763384||1.64E-07 |- | SP_PIR_KEYWORDS||Transcription||12||92.30769231||2.38E-10||8.573338781||2.08E-07 |- | GOTERM_BP_FAT||GO:0045449~regulation of transcription||12||92.30769231||1.30E-08||5.201076509||1.72E-05 |- | SP_PIR_KEYWORDS||nucleus||13||100||1.47E-08||4.491010974||1.28E-05 |- | GOTERM_MF_FAT||GO:0016564~transcription repressor activity||7||53.84615385||8.27E-08||23.96650844||8.10E-05 |- | GOTERM_MF_FAT||GO:0030528~transcription regulator activity||10||76.92307692||1.70E-07||7.15553351||1.67E-04 |- | GOTERM_BP_FAT||GO:0016481~negative regulation of transcription||7||53.84615385||5.90E-07||17.19244735||7.77E-04 |- | GOTERM_BP_FAT||GO:0010629~negative regulation of gene expression||7||53.84615385||1.02E-06||15.65740741||0.001345482 |- | GOTERM_BP_FAT||GO:0045934~negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process||7||53.84615385||1.12E-06||15.41276042||0.001475649 |- | GOTERM_BP_FAT||GO:0051172~negative regulation of nitrogen compound metabolic process||7||53.84615385||1.21E-06||15.20488118||0.001597891 |- | GOTERM_MF_FAT||GO:0008134~transcription factor binding||7||53.84615385||1.44E-06||14.76299545||0.001412732 |- | GOTERM_BP_FAT||GO:0010558~negative regulation of macromolecule biosynthetic process||7||53.84615385||1.65E-06||14.42656917||0.002173387 |- | GOTERM_BP_FAT||GO:0031327~negative regulation of cellular biosynthetic process||7||53.84615385||1.92E-06||14.06654783||0.002519407 |- | GOTERM_BP_FAT||GO:0006350~transcription||10||76.92307692||2.11E-06||5.365698874||0.002778119 |- | GOTERM_BP_FAT||GO:0009890~negative regulation of biosynthetic process||7||53.84615385||2.17E-06||13.77196044||0.002850924 |- | GOTERM_CC_FAT||GO:0005654~nucleoplasm||7||53.84615385||2.64E-06||11.27160494||0.002668839 |- | SP_PIR_KEYWORDS||repressor||6||46.15384615||4.02E-06||20.40848806||0.003505542 |- | GOTERM_CC_FAT||GO:0044451~nucleoplasm part||6||46.15384615||7.61E-06||15.35375375||0.007709187 |- | GOTERM_BP_FAT||GO:0010605~negative regulation of macromolecule metabolic process||7||53.84615385||9.13E-06||10.75113533||0.012014286 |- | GOTERM_BP_FAT||GO:0006355~regulation of transcription, DNA-dependent||9||69.23076923||9.79E-06||5.72250423||0.012881602 |- | GOTERM_BP_FAT||GO:0051252~regulation of RNA metabolic process||9||69.23076923||1.16E-05||5.596249311||0.015267288 |- | UP_SEQ_FEATURE||domain:Leucine-zipper||4||30.76923077||3.93E-05||53.46293706||0.04077532 |- | SP_PIR_KEYWORDS||dna-binding||8||61.53846154||4.11E-05||6.336682589||0.035859411 |- | GOTERM_CC_FAT||GO:0031981~nuclear lumen||7||53.84615385||4.82E-05||6.856245211||0.04883162 |- |}
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