Coexpression cluster:C2540

Full id: C2540_small_neuroblastoma_nonsmall_Urothelial_colon_anaplastic_Smooth

Phase1 CAGE Peaks

Hg19::chr1:165796753..165796776,+	p5@UCK2
Hg19::chr1:165796782..165796803,+	p2@UCK2
Hg19::chr1:165796811..165796860,+	p1@UCK2
Hg19::chr1:165796870..165796886,+	p4@UCK2

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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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>

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Cell Type

Ontology term	p-value	n
epithelial cell	5.93e-32	254
animal cell	3.78e-23	679
eukaryotic cell	3.78e-23	679
embryonic cell	9.36e-23	248
squamous epithelial cell	8.83e-11	62
non-terminally differentiated cell	1.41e-10	180
native cell	1.56e-10	722
mesodermal cell	4.31e-09	119
endo-epithelial cell	7.55e-08	43
endodermal cell	2.31e-07	59

Uber Anatomy

Ontology term	p-value	n
mesenchyme	1.01e-14	238
entire embryonic mesenchyme	1.01e-14	238
trunk mesenchyme	4.01e-09	143
endoderm-derived structure	6.87e-09	169
endoderm	6.87e-09	169
presumptive endoderm	6.87e-09	169
trunk	7.57e-09	216
cell layer	1.04e-08	312
epithelium	3.74e-08	309
multilaminar epithelium	5.89e-08	82
unilaminar epithelium	8.05e-08	138
epithelial tube	9.02e-08	118
multi-tissue structure	1.21e-07	347
respiratory primordium	1.22e-07	38
endoderm of foregut	1.22e-07	38
segment of respiratory tract	1.61e-07	46
larynx	2.21e-07	9
respiratory system	2.96e-07	72
respiratory tract	7.26e-07	53
digestive system	9.51e-07	155
digestive tract	9.51e-07	155
primitive gut	9.51e-07	155

Disease

Ontology term	p-value	n
cancer	9.56e-28	235
disease of cellular proliferation	2.57e-27	239
cell type cancer	7.18e-18	143
carcinoma	2.30e-14	106
organ system cancer	1.25e-10	137

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
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00512333429994634
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00817599460367645
CTCFL#140690	4	19.7464743589744	6.5732084880439e-06	0.000192999528052521
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106510009453125
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00997138388439793
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101474062120348
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160951504136921
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00390367735861466
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186162151389584
NFYA#4800	4	18.4255806998305	8.67100748407158e-06	0.000234548394361293
NFYB#4801	4	16.7597932535365	1.26678572070404e-05	0.000311518327959994
NR2C2#7182	4	32.6146109052409	8.82887529809196e-07	3.81971378317078e-05
SMARCB1#6598	4	18.2527157811574	9.00423392720929e-06	0.000241560027517033
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322396713332113
TAF7#6879	4	11.4330694049239	5.85061525419808e-05	0.000969584904051402
TAL1#6886	2	14.9343083387201	0.00642807757788807	0.0279492920131995
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244366673704834
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00508129809941719

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.