Coexpression cluster:C262

Full id: C262_breast_MCF7_skeletal_Reticulocytes_mucinous_hepatoblastoma_Wilms

Phase1 CAGE Peaks

Hg19::chr10:19498407..19498415,+	p@chr10:19498407..19498415 +
Hg19::chr10:19498455..19498482,+	p@chr10:19498455..19498482 +
Hg19::chr10:19498507..19498511,+	p@chr10:19498507..19498511 +
Hg19::chr10:19498541..19498551,+	p@chr10:19498541..19498551 +
Hg19::chr10:19498568..19498573,+	p@chr10:19498568..19498573 +
Hg19::chr10:19520550..19520559,+	p@chr10:19520550..19520559 +
Hg19::chr10:19832379..19832382,+	p@chr10:19832379..19832382 +
Hg19::chr10:8904309..8904317,+	p@chr10:8904309..8904317 +
Hg19::chr10:9012087..9012100,+	p1@ENST00000456526
Hg19::chr10:9012105..9012111,+	p3@ENST00000456526
Hg19::chr10:9012128..9012139,+	p2@ENST00000456526
Hg19::chr10:9238697..9238718,-	p@chr10:9238697..9238718 -
Hg19::chr11:131766993..131767004,-	p2@ENST00000419440
Hg19::chr11:131767210..131767232,-	p1@ENST00000419440
Hg19::chr11:18283431..18283456,+	p1@ST13P5
Hg19::chr11:85539944..85539950,+	p@chr11:85539944..85539950 +
Hg19::chr12:116933204..116933236,-	p@chr12:116933204..116933236 -
Hg19::chr13:23500751..23500764,+	p@chr13:23500751..23500764 +
Hg19::chr13:23500789..23500796,+	p@chr13:23500789..23500796 +
Hg19::chr13:23583578..23583586,+	p@chr13:23583578..23583586 +
Hg19::chr13:23733194..23733206,+	p@chr13:23733194..23733206 +
Hg19::chr17:38843592..38843605,+	p@chr17:38843592..38843605 +
Hg19::chr17:57184136..57184156,-	p4@TRIM37
Hg19::chr17:57970469..57970506,+	p1@RPS6KB1
Hg19::chr1:207038965..207038969,+	p1@IL20
Hg19::chr20:47538238..47538278,+	p1@ARFGEF2
Hg19::chr20:47538312..47538323,+	p3@ARFGEF2
Hg19::chr20:49348109..49348123,+	p1@PARD6B
Hg19::chr20:57429114..57429123,+	p66@GNAS
Hg19::chr20:57429157..57429163,+	p59@GNAS
Hg19::chr21:41755024..41755027,+	p2@DSCAM-AS1
Hg19::chr21:41755185..41755210,+	p1@DSCAM-AS1
Hg19::chr21:41756567..41756583,-	p@chr21:41756567..41756583 -
Hg19::chr2:11674163..11674179,+	p9@GREB1
Hg19::chr2:11674213..11674225,+	p11@GREB1
Hg19::chr2:11679852..11679866,+	p18@GREB1
Hg19::chr2:11732328..11732334,+	p@chr2:11732328..11732334 +
Hg19::chr2:11745301..11745305,+	p@chr2:11745301..11745305 +
Hg19::chr2:132301072..132301097,+	p@chr2:132301072..132301097 +
Hg19::chr2:132301109..132301133,+	p@chr2:132301109..132301133 +
Hg19::chr2:237768815..237768844,+	p@chr2:237768815..237768844 +
Hg19::chr3:129226494..129226510,+	p@chr3:129226494..129226510 +
Hg19::chr3:129226514..129226531,+	p@chr3:129226514..129226531 +
Hg19::chr3:63849694..63849740,-	p2@THOC7
Hg19::chr3:63849743..63849781,-	p3@THOC7
Hg19::chr3:64009102..64009184,-	p1@PSMD6
Hg19::chr5:177505250..177505293,-	p@chr5:177505250..177505293 -
Hg19::chr6:151937957..151937962,-	p@chr6:151937957..151937962 -
Hg19::chr9:1470588..1470601,+	p@chr9:1470588..1470601 +
Hg19::chr9:83986187..83986191,-	p@chr9:83986187..83986191 -

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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GO ID	GO name	FDR corrected p-value
GO:0045517	interleukin-20 receptor binding	0.0181900678706479
GO:0031852	mu-type opioid receptor binding	0.0181900678706479
GO:0031628	opioid receptor binding	0.0181900678706479
GO:0045616	regulation of keratinocyte differentiation	0.0181900678706479
GO:0045606	positive regulation of epidermal cell differentiation	0.0181900678706479
GO:0045684	positive regulation of epidermis development	0.0181900678706479
GO:0045618	positive regulation of keratinocyte differentiation	0.0181900678706479
GO:0005737	cytoplasm	0.0181900678706479
GO:0042517	positive regulation of tyrosine phosphorylation of Stat3 protein	0.0218069442542464
GO:0045604	regulation of epidermal cell differentiation	0.0363149639583208
GO:0046427	positive regulation of JAK-STAT cascade	0.0363149639583208
GO:0042531	positive regulation of tyrosine phosphorylation of STAT protein	0.0363149639583208
GO:0045682	regulation of epidermis development	0.0363149639583208
GO:0017022	myosin binding	0.0363149639583208
GO:0006510	ATP-dependent proteolysis	0.0363149639583208
GO:0042516	regulation of tyrosine phosphorylation of Stat3 protein	0.0363149639583208
GO:0032940	secretion by cell	0.0363149639583208
GO:0042503	tyrosine phosphorylation of Stat3 protein	0.0363149639583208
GO:0042509	regulation of tyrosine phosphorylation of STAT protein	0.0447089513687611
GO:0007043	intercellular junction assembly	0.045211431643751
GO:0046425	regulation of JAK-STAT cascade	0.045211431643751
GO:0042383	sarcolemma	0.045211431643751
GO:0046903	secretion	0.045211431643751
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	0.045211431643751
GO:0007260	tyrosine phosphorylation of STAT protein	0.045211431643751
GO:0045216	intercellular junction assembly and maintenance	0.045211431643751
GO:0030054	cell junction	0.0494088084778299

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	4.84e-07	254

Uber Anatomy

Ontology term	p-value	n
adult organism	4.75e-12	115
subdivision of digestive tract	1.17e-09	129
endodermal part of digestive tract	1.17e-09	129
digestive system	1.55e-09	155
digestive tract	1.55e-09	155
primitive gut	1.55e-09	155
endoderm-derived structure	1.31e-08	169
endoderm	1.31e-08	169
presumptive endoderm	1.31e-08	169
mixed endoderm/mesoderm-derived structure	3.74e-08	130
foregut	3.70e-07	98
endo-epithelium	4.87e-07	82

Disease

Ontology term	p-value	n
cell type cancer	2.11e-37	143
carcinoma	1.03e-31	106
cancer	8.90e-31	235
disease of cellular proliferation	4.30e-29	239
adenocarcinoma	9.49e-12	25
organ system cancer	1.44e-09	137
disease of anatomical entity	4.82e-09	39

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
EP300#2033	17	2.30314018691589	0.000547340073535136	0.004725830848209
ESR1#2099	7	4.30760446146163	0.00111884438245137	0.00767242209184755
FOXA1#3169	11	2.4379123448648	0.00436569357158959	0.0206938987393113
GATA3#2625	9	4.90257294429708	7.7121315201363e-05	0.00118920316526135
MYC#4609	17	1.7755758363472	0.009416151877473	0.0355253769934038

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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