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Coexpression cluster:C3074: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189120377290851!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114922313063531!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320398492236822!GATA2#2624;3:12.744931733554:0.000482952770428379:0.0043590963953651!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000848549307669937!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00432711336157518!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185729351109396!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268584528948364!REST#5978;3:9.65002871612802:0.00111263624711459:0.00765246078448473!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027539061509742!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00202566514011881!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00540508947174473!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00627670159772077!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00612956553951428!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327909378279816
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189120377290851!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114922313063531!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320398492236822!GATA2#2624;3:12.744931733554:0.000482952770428379:0.0043590963953651!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000848549307669937!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00432711336157518!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185729351109396!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268584528948364!REST#5978;3:9.65002871612802:0.00111263624711459:0.00765246078448473!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027539061509742!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00202566514011881!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00540508947174473!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00627670159772077!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00612956553951428!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327909378279816
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}}
}}

Revision as of 15:54, 26 November 2012


Full id: C3074_Fibroblast_epithelioid_mesenchymal_Adipocyte_Hair_Smooth_Olfactory



Phase1 CAGE Peaks

Hg19::chr11:10326862..10326874,+p7@ADM
Hg19::chr11:10326893..10326913,+p6@ADM
Hg19::chr11:10326918..10326933,+p3@ADM


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>disease_data<br>


Cell Type
Ontology termp-valuen
fibroblast7.56e-1676
skin fibroblast1.13e-1423
fat cell2.16e-0815
animal cell3.63e-07679
eukaryotic cell3.63e-07679
multi fate stem cell4.12e-07427
stem cell5.25e-07441
somatic cell7.72e-07588
Uber Anatomy
Ontology termp-valuen
skin of body1.63e-1241
integument1.81e-1246
integumental system1.81e-1246
surface structure2.90e-0999
Disease
Ontology termp-valuen
musculoskeletal system disease6.20e-075
myotonic disease6.20e-075
muscle tissue disease6.20e-075
myopathy6.20e-075
muscular disease6.20e-075
myotonic dystrophy6.20e-075


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
CCNT2#90536.336201576962630.003930750035764890.0189120377290851
CEBPB#105137.971147625824820.001974187055288560.0114922313063531
E2F6#187635.017155731697390.00791769806886330.0320398492236822
GATA2#2624312.7449317335540.0004829527704283790.0043590963953651
GATA3#2625327.2365163572064.94721007899563e-050.000848549307669937
GTF2F1#2962312.73966087675770.0004835525047438590.00432711336157518
MAX#414936.452555509007120.003721913834265510.0185729351109396
NFKB1#479035.488063424193840.006049381815655430.0268584528948364
REST#597839.650028716128020.001112636247114590.00765246078448473
SIN3A#2594235.408884726815140.006318961977991520.027539061509742
SMARCB1#6598318.25271578115740.000164397760679890.00202566514011881
TAF7#6879311.43306940492390.0006690181981945830.00540508947174473
TCF12#6938310.63446490218640.0008313523990202070.00627670159772077
TFAP2C#7022310.80922860986020.0007916746575753130.00612956553951428
YY1#752834.911170749853860.008441455341808260.0327909378279816



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.