Coexpression cluster:C3635

Full id: C3635_testicular_hepatoblastoma_hepatocellular_lung_gastric_prostate_Trabecular

Phase1 CAGE Peaks

Hg19::chr17:41623667..41623682,-	p8@ETV4
Hg19::chr17:41623692..41623715,-	p1@ETV4
Hg19::chr17:41623716..41623727,-	p12@ETV4

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	8.14e-37	254
embryonic cell	6.62e-26	248
animal cell	6.48e-12	679
eukaryotic cell	6.48e-12	679
endodermal cell	1.00e-09	59
squamous epithelial cell	9.22e-09	62
ectodermal cell	3.57e-08	71
endo-epithelial cell	3.99e-08	43
non-terminally differentiated cell	5.26e-08	180
mesodermal cell	1.65e-07	119

Uber Anatomy

Ontology term	p-value	n
cell layer	1.79e-13	312
epithelium	1.42e-12	309
mesenchyme	1.51e-11	238
entire embryonic mesenchyme	1.51e-11	238
epithelial tube	2.06e-11	118
multi-tissue structure	3.02e-11	347
endoderm-derived structure	5.77e-10	169
endoderm	5.77e-10	169
presumptive endoderm	5.77e-10	169
unilaminar epithelium	2.61e-09	138
trunk	6.22e-09	216
primordium	7.90e-09	168
trunk mesenchyme	1.30e-08	143
digestive system	2.08e-08	155
digestive tract	2.08e-08	155
primitive gut	2.08e-08	155
organism subdivision	3.87e-08	365
immaterial anatomical entity	5.07e-08	126
anatomical cluster	7.54e-08	286
trunk region element	1.45e-07	107
mixed endoderm/mesoderm-derived structure	1.95e-07	130
simple squamous epithelium	2.06e-07	22
anatomical conduit	2.28e-07	241
vasculature	2.81e-07	79
vascular system	2.81e-07	79
endo-epithelium	8.14e-07	82

Disease

Ontology term	p-value	n
cancer	5.21e-15	235
disease of cellular proliferation	4.28e-14	239
carcinoma	4.35e-13	106
cell type cancer	2.90e-12	143

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	3	6.33620157696263	0.00393075003576489	0.0189837504270635
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320232755311204
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00761458762032282
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.0058081370147361
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127930949978159
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199387975511413
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245562305512766
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276336182069951
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00612968797025102

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.