Coexpression cluster:C4202

Full id: C4202_Hepatic_Astrocyte_testicular_teratocarcinoma_synovial_basal_prostate

Phase1 CAGE Peaks

Hg19::chr2:237076971..237076978,-	p3@GBX2
Hg19::chr2:237076992..237077008,-	p2@GBX2
Hg19::chr2:237077022..237077038,-	p1@GBX2

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

---

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

---

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>

---

Cell Type

Ontology term	p-value	n
epithelial cell	1.40e-14	253
lining cell	8.08e-12	58
barrier cell	8.08e-12	58
endothelial cell of artery	1.09e-11	9
blood vessel endothelial cell	5.24e-11	18
embryonic blood vessel endothelial progenitor cell	5.24e-11	18
endothelial cell of vascular tree	3.22e-10	24
squamous epithelial cell	1.62e-09	63
endothelial cell	3.77e-09	36
embryonic stem cell	1.32e-08	5
meso-epithelial cell	1.72e-08	45
aortic endothelial cell	3.02e-07	6

Uber Anatomy

Ontology term	p-value	n
posterior neural tube	1.64e-15	15
chordal neural plate	1.64e-15	15
segmental subdivision of hindbrain	3.29e-14	12
hindbrain	3.29e-14	12
presumptive hindbrain	3.29e-14	12
segmental subdivision of nervous system	6.94e-13	13
endothelial tube	1.09e-11	9
arterial system endothelium	1.09e-11	9
endothelium of artery	1.09e-11	9
blood vessel endothelium	5.24e-11	18
endothelium	5.24e-11	18
cardiovascular system endothelium	5.24e-11	18
regional part of metencephalon	1.80e-10	9
metencephalon	1.80e-10	9
future metencephalon	1.80e-10	9
brainstem	1.53e-08	6
squamous epithelium	1.68e-08	25
central nervous system	1.70e-08	81
simple squamous epithelium	2.08e-08	22
nervous system	4.07e-08	89
neural tube	6.95e-08	56
neural rod	6.95e-08	56
future spinal cord	6.95e-08	56
neural keel	6.95e-08	56
tube	1.86e-07	192
cerebellum	2.52e-07	6
rhombic lip	2.52e-07	6
brain	3.17e-07	68
future brain	3.17e-07	68
regional part of nervous system	9.04e-07	53
regional part of brain	9.04e-07	53

Disease

Ontology term	p-value	n
cell type cancer	9.08e-11	143
carcinoma	5.85e-10	106
cancer	1.58e-08	235
disease of cellular proliferation	4.85e-08	239

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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.00129802898279646
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326289361450533
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323140472299341
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186998104073149
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000739095875017222
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246325937737816
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190775202649526
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00422330360892503

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

---

This analysis result is provided for C0 - C305 clusters.