Coexpression cluster:C356

Full id: C356_renal_Smooth_Chondrocyte_thyroid_serous_Small_mesenchymal

Phase1 CAGE Peaks

Hg19::chr10:102106384..102106429,+	p15@SCD
Hg19::chr10:75532821..75532859,+	p@chr10:75532821..75532859 +
Hg19::chr12:105286070..105286074,-	p@chr12:105286070..105286074 -
Hg19::chr12:125398498..125398506,-	p16@UBC
Hg19::chr12:125398630..125398643,-	p4@UBC
Hg19::chr19:41882466..41882478,+	p9@TMEM91
Hg19::chr19:41882598..41882689,+	p3@TMEM91
Hg19::chr1:16353510..16353514,+	p@chr1:16353510..16353514 +
Hg19::chr21:35445827..35445886,+	p1@MRPS6 p1@SLC5A3
Hg19::chr21:35452404..35452441,+	p@chr21:35452404..35452441 +
Hg19::chr21:35454368..35454370,+	p@chr21:35454368..35454370 +
Hg19::chr21:35470304..35470310,+	p@chr21:35470304..35470310 +
Hg19::chr21:35484158..35484164,+	p@chr21:35484158..35484164 +
Hg19::chr21:35495858..35495862,+	p4@MRPS6
Hg19::chr21:35496814..35496818,+	p@chr21:35496814..35496818 +
Hg19::chr21:41029235..41029269,+	p2@B3GALT5
Hg19::chr2:70780951..70780966,-	p1@TGFA
Hg19::chr2:70781087..70781098,-	p2@TGFA
Hg19::chr4:188508175..188508193,-	p@chr4:188508175..188508193 -
Hg19::chr5:159659030..159659074,+	p3@FABP6
Hg19::chr6:15526561..15526569,+	p@chr6:15526561..15526569 +
Hg19::chr6:43737939..43737956,+	p1@VEGFA
Hg19::chr6:43745444..43745451,+	p13@VEGFA
Hg19::chr6:43745909..43745939,+	p15@VEGFA
Hg19::chr6:43746193..43746214,+	p6@VEGFA
Hg19::chr6:43752516..43752532,+	p4@VEGFA
Hg19::chr6:43753591..43753612,+	p@chr6:43753591..43753612 +
Hg19::chr7:125078119..125078156,+	p2@ENST00000458437
Hg19::chr7:47579188..47579231,-	p13@TNS3
Hg19::chr8:134250145..134250165,-	p13@NDRG1
Hg19::chr8:25337575..25337596,+	p@chr8:25337575..25337596 +

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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p.value	FDR	nGenes	nPathway	Name
1.74727516305728e-06	0.00110602517821526	3	71	PPAR signaling pathway (KEGG):03320

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:0042127	regulation of cell proliferation	0.0151338388640772
GO:0001525	angiogenesis	0.0151338388640772
GO:0048514	blood vessel morphogenesis	0.0151338388640772
GO:0008283	cell proliferation	0.0151338388640772
GO:0048646	anatomical structure formation	0.0151338388640772
GO:0009967	positive regulation of signal transduction	0.0151338388640772
GO:0001568	blood vessel development	0.0151338388640772
GO:0001944	vasculature development	0.0151338388640772
GO:0005155	epidermal growth factor receptor activating ligand activity	0.0151338388640772
GO:0050840	extracellular matrix binding	0.0151338388640772
GO:0005172	vascular endothelial growth factor receptor binding	0.0151338388640772
GO:0045741	positive regulation of epidermal growth factor receptor activity	0.0151338388640772
GO:0004768	stearoyl-CoA 9-desaturase activity	0.0151338388640772
GO:0030949	positive regulation of vascular endothelial growth factor receptor signaling pathway	0.0151338388640772
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0155861889547463
GO:0030947	regulation of vascular endothelial growth factor receptor signaling pathway	0.0165509309304655
GO:0008284	positive regulation of cell proliferation	0.0168920544335655
GO:0001948	glycoprotein binding	0.0176415992128267
GO:0008083	growth factor activity	0.0176415992128267
GO:0008499	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity	0.0176415992128267
GO:0045742	positive regulation of epidermal growth factor receptor signaling pathway	0.0176415992128267
GO:0050930	induction of positive chemotaxis	0.0176415992128267
GO:0007176	regulation of epidermal growth factor receptor activity	0.0176415992128267
GO:0007167	enzyme linked receptor protein signaling pathway	0.0176415992128267
GO:0005154	epidermal growth factor receptor binding	0.0176415992128267
GO:0048531	beta-1,3-galactosyltransferase activity	0.0176415992128267
GO:0050926	regulation of positive chemotaxis	0.0176415992128267
GO:0050927	positive regulation of positive chemotaxis	0.0176415992128267
GO:0050918	positive chemotaxis	0.0176415992128267
GO:0004708	MAP kinase kinase activity	0.0176415992128267
GO:0048010	vascular endothelial growth factor receptor signaling pathway	0.0176415992128267
GO:0004712	protein serine/threonine/tyrosine kinase activity	0.0176415992128267
GO:0050921	positive regulation of chemotaxis	0.0176415992128267
GO:0050920	regulation of chemotaxis	0.0176415992128267
GO:0016717	oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water	0.0176415992128267
GO:0045840	positive regulation of mitosis	0.0176415992128267
GO:0009887	organ morphogenesis	0.0181039866972444
GO:0042058	regulation of epidermal growth factor receptor signaling pathway	0.0181039866972444
GO:0035250	UDP-galactosyltransferase activity	0.0230579040204921
GO:0050679	positive regulation of epithelial cell proliferation	0.023220920115621
GO:0001570	vasculogenesis	0.023220920115621
GO:0045787	positive regulation of progression through cell cycle	0.0302053811995919
GO:0031177	phosphopantetheine binding	0.0324452868894586
GO:0005615	extracellular space	0.0324452868894586
GO:0050678	regulation of epithelial cell proliferation	0.035217840976197
GO:0005504	fatty acid binding	0.035596977264209
GO:0007173	epidermal growth factor receptor signaling pathway	0.0360018094262514
GO:0050673	epithelial cell proliferation	0.0360018094262514
GO:0042221	response to chemical stimulus	0.0360018094262514
GO:0010038	response to metal ion	0.0369596962407415
GO:0016020	membrane	0.039237620499413
GO:0008378	galactosyltransferase activity	0.0405941435874171
GO:0010035	response to inorganic substance	0.0418110153633352
GO:0001666	response to hypoxia	0.0468701625904609

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
endodermal cell	1.75e-09	59
endo-epithelial cell	5.38e-08	43

Uber Anatomy

Ontology term	p-value	n
organ	1.70e-12	511
embryo	5.19e-09	612
anatomical group	3.23e-08	626
embryonic structure	3.74e-08	605
developing anatomical structure	3.74e-08	605
anatomical system	4.91e-08	625
multi-cellular organism	6.01e-08	659
germ layer	7.32e-08	604
embryonic tissue	7.32e-08	604
presumptive structure	7.32e-08	604
epiblast (generic)	7.32e-08	604

Disease

Ontology term	p-value	n
carcinoma	4.35e-09	106
cell type cancer	4.87e-09	143
female reproductive organ cancer	4.09e-08	27
reproductive organ cancer	1.82e-07	29

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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No analysis results for this cluster

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.