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Coexpression cluster:C3661: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;2:16.2385345282024:0.00491746240780997:0.0229982918995686!BCL3#602;2:23.0314018691589:0.00246467476084291:0.0138510636756173!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273821087866143!BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296237439966597!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401920812573902!FOSL1#8061;2:26.4757198109153:0.00186983370259098:0.0110248722443911!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376685503655221!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155796777562847!JUNB#3726;2:20.4070884398808:0.00313146219943874:0.0164477359005825!KAT2A#2648;2:410.726666666667:7.8689746933917e-06:0.00022229587449368!MAFF#23764;2:37.5435709932968:0.000934477401556032:0.00676903074914068!MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191094528149208!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324844479398681!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268256584519638!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457363448120282!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.028751751847863!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.00560821729455154!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390080609785663!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329046908073651!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190086838516255!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328973899937726
|tf_chipseq_enrich=BATF#10538;2:16.2385345282024:0.00491746240780997:0.0229982918995686!BCL3#602;2:23.0314018691589:0.00246467476084291:0.0138510636756173!BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273821087866143!BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296237439966597!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401920812573902!FOSL1#8061;2:26.4757198109153:0.00186983370259098:0.0110248722443911!FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376685503655221!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155796777562847!JUNB#3726;2:20.4070884398808:0.00313146219943874:0.0164477359005825!KAT2A#2648;2:410.726666666667:7.8689746933917e-06:0.00022229587449368!MAFF#23764;2:37.5435709932968:0.000934477401556032:0.00676903074914068!MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191094528149208!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324844479398681!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268256584519638!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457363448120282!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.028751751847863!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.00560821729455154!TFAP2A#7020;2:11.0124229153633:0.0105499065521556:0.0390080609785663!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329046908073651!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190086838516255!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328973899937726
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}}
}}

Revision as of 16:16, 26 November 2012


Full id: C3661_CD14_Small_Fibroblast_Preadipocyte_serous_MCF7_Mast



Phase1 CAGE Peaks

Hg19::chr17:57915281..57915332,+p1@AK310806
Hg19::chr17:57915475..57915493,+p@chr17:57915475..57915493
+
Hg19::chr17:57921459..57921462,+p@chr17:57921459..57921462
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
bone marrow9.08e-1476
immune system1.10e-1293
bone element2.71e-1282
skeletal element8.91e-1290
hemolymphoid system7.23e-11108
hematopoietic system8.85e-1198
blood island8.85e-1198
skeletal system1.01e-10100
musculoskeletal system1.44e-09167


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#10538216.23853452820240.004917462407809970.0229982918995686
BCL3#602223.03140186915890.002464674760842910.0138510636756173
BCLAF1#9774214.43509840674790.006201147435546130.0273821087866143
BRCA1#672213.45615376214920.007119807716084560.0296237439966597
ELK4#2005210.8237877723120.01091284719516480.0401920812573902
FOSL1#8061226.47571981091530.001869833702590980.0110248722443911
FOSL2#2355211.28680040304110.0100534586973120.0376685503655221
GTF2B#2959221.29588662288280.002878180589911410.0155796777562847
JUNB#3726220.40708843988080.003131462199438740.0164477359005825
KAT2A#26482410.7266666666677.8689746933917e-060.00022229587449368
MAFF#23764237.54357099329680.0009344774015560320.00676903074914068
MAFK#7975218.06715542521990.003983674744936810.0191094528149208
MEF2A#4205212.4954872730960.008235029478029740.0324844479398681
PBX3#5090214.60967512449610.006056122473217890.0268256584519638
SMC3#9126210.02995522995520.0126656379767470.0457363448120282
STAT1#6772213.80439166479950.006770931708444080.028751751847863
STAT2#6773243.50918079096040.0006968990898868230.00560821729455154
TFAP2A#7020211.01242291536330.01054990655215560.0390080609785663
TRIM28#10155212.39368336350830.008368344129438470.0329046908073651
USF1#739136.361499277207960.00388404057290560.0190086838516255
YY1#752834.911170749853860.008441455341808260.0328973899937726



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.