Coexpression cluster:C2050

Full id: C2050_chronic_acute_prostate_large_Mast_nonsmall_breast

Phase1 CAGE Peaks

Hg19::chr10:22605374..22605387,+	p2@COMMD3 p4@BMI1
Hg19::chr10:22605396..22605408,+	p3@COMMD3 p9@BMI1
Hg19::chr10:22605437..22605446,+	p14@BMI1 p4@COMMD3
Hg19::chr10:22610271..22610284,+	p7@BMI1

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0007379	segment specification	0.0100654842000056
GO:0048146	positive regulation of fibroblast proliferation	0.0100654842000056
GO:0048144	fibroblast proliferation	0.0100654842000056
GO:0048145	regulation of fibroblast proliferation	0.0100654842000056
GO:0035282	segmentation	0.0156537320258094
GO:0009880	embryonic pattern specification	0.0156537320258094
GO:0003002	regionalization	0.0416538239019674

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><br><br>disease_data<br>

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Disease

Ontology term	p-value	n
myeloid leukemia	1.69e-11	31
leukemia	4.13e-09	39
hematologic cancer	1.13e-07	51
immune system cancer	1.13e-07	51
disease of cellular proliferation	3.55e-07	239

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

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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

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

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	3	16.8473808945066	0.000340998682365564	0.00346300674713897
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00511040168989678
CTBP2#1488	3	47.0377502544961	1.60047699357395e-05	0.00037013334085888
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106214706807756
E2F4#1874	3	9.50104523646333	0.00185075103472827	0.0109228406032993
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00994731004595177
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101206159880261
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160487995030883
ETS1#2113	3	7.29657069165175	0.0040085737751139	0.0191953891104595
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.037834715505546
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00247692937737931
MAX#4149	3	4.83941663175534	0.0131573713783684	0.0465858463364211
NFE2#4778	3	57.9031954887218	8.59734810665173e-06	0.00023352365121212
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00766242564767439
NR2C2#7182	3	24.4609581789307	0.000112590606343803	0.00155478650481825
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434659924318322
REST#5978	3	7.23752153709602	0.00410469730419261	0.0195668666645019
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00793875297403831
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321059686796522
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243388217801849
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00506917860959508
USF2#7392	4	12.9921973850696	3.50833029870167e-05	0.000680041774435975
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342162001696712
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00247991185444005

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

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This analysis result is provided for C0 - C305 clusters.