Coexpression cluster:C4533

Full id: C4533_lung_gall_rectal_salivary_Prostate_Keratinocyte_amniotic

Phase1 CAGE Peaks

Hg19::chr5:95998673..95998713,+	p7@CAST
Hg19::chr5:95998714..95998744,+	p5@CAST
Hg19::chr5:95998746..95998764,+	p12@CAST

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
endo-epithelial cell	1.81e-15	43
endodermal cell	8.90e-14	59
epithelial cell	2.45e-12	254
epithelial cell of alimentary canal	1.02e-07	21
vascular associated smooth muscle cell	6.01e-07	32
embryonic cell	9.87e-07	248

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	8.93e-19	169
endoderm	8.93e-19	169
presumptive endoderm	8.93e-19	169
digestive system	7.60e-16	155
digestive tract	7.60e-16	155
primitive gut	7.60e-16	155
mesenchyme	1.11e-13	238
entire embryonic mesenchyme	1.11e-13	238
subdivision of digestive tract	1.62e-12	129
endodermal part of digestive tract	1.62e-12	129
respiratory system	1.71e-11	72
mixed endoderm/mesoderm-derived structure	1.86e-11	130
trunk	1.25e-10	216
anatomical system	3.51e-10	625
anatomical group	5.05e-10	626
multi-cellular organism	9.00e-10	659
multi-tissue structure	1.39e-09	347
surface structure	4.18e-09	95
female organism	5.66e-09	41
respiratory tract	1.05e-08	53
organ	1.15e-08	511
mesoderm	2.50e-08	448
mesoderm-derived structure	2.50e-08	448
presumptive mesoderm	2.50e-08	448
orifice	3.20e-08	35
organism subdivision	5.76e-08	365
multilaminar epithelium	7.64e-08	82
respiratory primordium	2.05e-07	38
endoderm of foregut	2.05e-07	38
female reproductive organ	3.45e-07	37
female reproductive system	3.45e-07	37
segment of respiratory tract	4.03e-07	46
embryonic structure	7.48e-07	605
developing anatomical structure	7.48e-07	605
reproductive structure	7.54e-07	59
reproductive system	7.54e-07	59
unilaminar epithelium	8.95e-07	138

Disease

Ontology term	p-value	n
carcinoma	1.16e-08	106

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	0.032728031432605
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00918502996012008
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464548701733733
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435735461975357
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157507264590792
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00473030672431246
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.0013730360952667
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203841122256287
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00376155801570202
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00249272829520452
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00618319694604458

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.