Coexpression cluster:C2874

Full id: C2874_mature_neuroblastoma_oral_pharyngeal_normal_neuroectodermal_mesothelioma

Phase1 CAGE Peaks

Hg19::chr7:116139649..116139711,+	p2@CAV2
Hg19::chr7:116139744..116139818,+	p1@CAV2
Hg19::chr7:116139821..116139832,+	p3@CAV2
Hg19::chr7:116140090..116140138,+	p4@CAV2

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><br>

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Cell Type

Ontology term	p-value	n
epithelial cell	5.60e-19	254
embryonic cell	1.09e-17	248
squamous epithelial cell	7.37e-16	62
mesodermal cell	6.73e-14	119
endothelial cell of vascular tree	3.56e-12	24
lining cell	2.16e-11	57
barrier cell	2.16e-11	57
fibroblast	2.01e-09	75
endothelial cell	3.00e-09	35
blood vessel endothelial cell	7.16e-09	18
embryonic blood vessel endothelial progenitor cell	7.16e-09	18
non-terminally differentiated cell	1.72e-08	180
meso-epithelial cell	5.35e-08	44
endo-epithelial cell	1.07e-07	43
fat cell	1.45e-07	15

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	9.40e-15	659
vessel	1.71e-12	69
vasculature	2.89e-12	79
vascular system	2.89e-12	79
trunk	3.21e-12	216
anatomical system	4.69e-12	625
splanchnic layer of lateral plate mesoderm	5.16e-12	84
anatomical group	5.72e-12	626
cell layer	8.41e-12	312
epithelium	1.13e-11	309
organism subdivision	1.35e-11	365
surface structure	1.69e-11	95
epithelial tube	4.28e-11	118
organ component layer	1.09e-10	57
unilaminar epithelium	1.36e-10	138
anatomical cluster	4.30e-10	286
mesenchyme	7.19e-10	238
entire embryonic mesenchyme	7.19e-10	238
blood vessel	9.25e-10	60
epithelial tube open at both ends	9.25e-10	60
blood vasculature	9.25e-10	60
vascular cord	9.25e-10	60
circulatory system	2.62e-09	113
anatomical conduit	2.67e-09	241
multi-tissue structure	2.75e-09	347
trunk mesenchyme	3.42e-09	143
simple squamous epithelium	4.13e-09	22
endoderm-derived structure	4.23e-09	169
endoderm	4.23e-09	169
presumptive endoderm	4.23e-09	169
endothelium	7.16e-09	18
blood vessel endothelium	7.16e-09	18
cardiovascular system endothelium	7.16e-09	18
cardiovascular system	1.48e-08	110
multilaminar epithelium	6.15e-08	82
extraembryonic membrane	6.41e-08	14
membranous layer	6.41e-08	14
squamous epithelium	1.28e-07	25
organ part	1.93e-07	219
integument	5.42e-07	45
integumental system	5.42e-07	45
somite	5.79e-07	83
paraxial mesoderm	5.79e-07	83
presomitic mesoderm	5.79e-07	83
presumptive segmental plate	5.79e-07	83
trunk paraxial mesoderm	5.79e-07	83
presumptive paraxial mesoderm	5.79e-07	83
embryonic structure	8.37e-07	605
developing anatomical structure	8.37e-07	605

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	0.0051363325317388
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186596405670175
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0387191590548422
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0107075416933143
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00347274429612611

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.