Coexpression cluster:C4266

Full id: C4266_immature_thyroid_Small_smallcell_Renal_chorionic_pancreas

Phase1 CAGE Peaks

Hg19::chr3:111805212..111805258,+	p1@C3orf52
Hg19::chr3:111805262..111805289,+	p2@C3orf52
Hg19::chr3:111805316..111805323,+	p4@C3orf52

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	1.23e-26	254
endo-epithelial cell	6.43e-12	43
embryonic cell	6.98e-09	248
endodermal cell	1.29e-08	59

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	3.13e-15	169
endoderm	3.13e-15	169
presumptive endoderm	3.13e-15	169
digestive system	2.41e-12	155
digestive tract	2.41e-12	155
primitive gut	2.41e-12	155
anatomical space	1.36e-11	104
subdivision of digestive tract	1.28e-10	129
endodermal part of digestive tract	1.28e-10	129
mesenchyme	5.40e-10	238
entire embryonic mesenchyme	5.40e-10	238
anatomical cavity	2.19e-09	70
reproductive structure	2.90e-09	59
reproductive system	2.90e-09	59
immaterial anatomical entity	3.83e-09	126
female organism	6.82e-09	41
body cavity precursor	9.90e-09	63
mixed endoderm/mesoderm-derived structure	1.72e-08	130
endo-epithelium	3.25e-08	82
primordium	3.83e-08	168
respiratory system	7.71e-08	72
multi-tissue structure	1.02e-07	347
reproductive organ	1.07e-07	48
female reproductive organ	1.09e-07	37
female reproductive system	1.09e-07	37
respiratory tract	3.08e-07	53
trunk	3.40e-07	216
renal system	5.82e-07	45
epithelial bud	6.17e-07	37
epithelial fold	6.37e-07	51
body cavity	7.85e-07	46
urinary system structure	8.23e-07	44

Disease

Ontology term	p-value	n
carcinoma	9.26e-19	106
cell type cancer	3.16e-13	143
reproductive organ cancer	4.68e-09	29
female reproductive organ cancer	8.61e-09	27
squamous cell carcinoma	1.26e-08	14
disease of cellular proliferation	4.27e-08	239
cancer	3.36e-07	235

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
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326494309506867
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323329997503036
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0187034094662395
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00721613305953624
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295331843485478
PRDM1#639	3	131.830955777461	4.35536935195671e-07	2.08369408955111e-05
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00615768566099476
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330280281138543
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140584842343134

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.