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Coexpression cluster:C3113: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259457734418352!BHLHE40#8553;2:29.9145423646516:0.00146748352710614:0.00939396335197295!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189163949398788!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00658480394660652!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.03236364081015!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00435463878720525!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032044815679675!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460124127392436!EP300#2033;3:6.7739417262232:0.00321688050010379:0.016686588981342!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00894883577924663!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00579454098306225!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153642985286604!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127624511859642!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000253040321747052!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156169178310235!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185764854928007!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.0019903133114787!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00244965622199172!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136042043174738!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00483054332374885!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275448086322241!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245448578152612!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000937615585039036!SREBF1#6720;2:31.3372329603255:0.0013381626513618:0.00887285690721702!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.005406344135039!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189545027519129!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327970371058782!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0377956819366885
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0.0228361,0.361435
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}}
}}

Revision as of 15:56, 26 November 2012


Full id: C3113_Smooth_Fibroblast_lymphangiectasia_colon_gall_mesenchymal_Chondrocyte



Phase1 CAGE Peaks


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




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




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>disease_data<br>



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



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
ATF3#467214.97544968400580.005768294540793880.0259457734418352
BHLHE40#8553229.91454236465160.001467483527106140.00939396335197295
CCNT2#90536.336201576962630.003930750035764890.0189163949398788
CHD2#1106310.34402283411690.0009033701102746880.00658480394660652
E2F1#186934.907389214879320.008460985347239390.03236364081015
E2F4#1874312.66806031528440.0004917987006298980.00435463878720525
E2F6#187635.017155731697390.00791769806886330.032044815679675
ELF1#199734.258097958807540.01295179875054610.0460124127392436
EP300#203336.77394172622320.003216880500103790.016686588981342
FOS#235338.99795530889440.001372499272417130.00894883577924663
FOXA1#3169311.08141974938550.000734755275698670.00579454098306225
GABPB1#255337.067683836182170.002832212825417420.0153642985286604
IRF1#365937.63716375356390.002244692747297240.0127624511859642
IRF3#3661346.98195221148969.63568551583244e-060.000253040321747052
JUND#372736.994663941871030.002921845042734990.0156169178310235
MAX#414936.452555509007120.003721913834265510.0185764854928007
NFYA#4800318.42558069983050.0001598135507814160.0019903133114787
NFYB#4801316.75979325353650.0002123649923296180.00244965622199172
PBX3#5090321.91451268674419.49854535978121e-050.00136042043174738
RFX5#5993312.04791082719510.0005717246050312580.00483054332374885
SIN3A#2594235.408884726815140.006318961977991520.0275448086322241
SP1#666735.69838137814090.005403962701712170.0245448578152612
SP2#6668326.15353049384465.58768218891694e-050.000937615585039036
SREBF1#6720231.33723296032550.00133816265136180.00887285690721702
TAF7#6879311.43306940492390.0006690181981945830.005406344135039
USF1#739136.361499277207960.00388404057290560.0189545027519129
YY1#752834.911170749853860.008441455341808260.0327970371058782
ZEB1#6935211.25895467836260.01010222676646330.0377956819366885



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.