Coexpression cluster:C2086

Full id: C2086_smooth_bladder_heart_gall_esophagus_seminal_uterus

Phase1 CAGE Peaks

Hg19::chr10:97197552..97197590,-	p9@SORBS1
Hg19::chr2:220284774..220284780,+	p10@DES
Hg19::chr2:220284788..220284812,+	p2@DES
Hg19::chr2:220284844..220284855,+	p8@DES

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
2.88643650599953e-06	0.0018271143082977	2	49	Muscle contraction (Reactome):REACT_17044

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:0045098	type III intermediate filament	0.00535727426246884
GO:0005915	zonula adherens	0.00535727426246884
GO:0007010	cytoskeleton organization and biogenesis	0.00749885925619792
GO:0043149	stress fiber formation	0.00749885925619792
GO:0001725	stress fiber	0.00749885925619792
GO:0032432	actin filament bundle	0.00749885925619792
GO:0044430	cytoskeletal part	0.00749885925619792
GO:0048041	focal adhesion formation	0.00749885925619792
GO:0005913	cell-cell adherens junction	0.00749885925619792
GO:0030018	Z disc	0.00749885925619792
GO:0042383	sarcolemma	0.00758779626979266
GO:0031674	I band	0.00758779626979266
GO:0051017	actin filament bundle formation	0.00765122132711095
GO:0005626	insoluble fraction	0.00765122132711095
GO:0005158	insulin receptor binding	0.00821194817254023
GO:0005856	cytoskeleton	0.00856785393064033
GO:0015758	glucose transport	0.00856785393064033
GO:0008645	hexose transport	0.00856785393064033
GO:0008286	insulin receptor signaling pathway	0.00856785393064033
GO:0015749	monosaccharide transport	0.00856785393064033
GO:0006996	organelle organization and biogenesis	0.00873810035451232
GO:0005924	cell-substrate adherens junction	0.00886120895483628
GO:0030055	cell-matrix junction	0.00886120895483628
GO:0007015	actin filament organization	0.00886120895483628
GO:0008016	regulation of heart contraction	0.00886120895483628
GO:0045121	lipid raft	0.00886120895483628
GO:0060047	heart contraction	0.00886120895483628
GO:0003015	heart process	0.00886120895483628
GO:0030017	sarcomere	0.00886120895483628
GO:0030016	myofibril	0.00932488368221589
GO:0005912	adherens junction	0.00932488368221589
GO:0044449	contractile fiber part	0.0100363141022865
GO:0043292	contractile fiber	0.0103803838974261
GO:0005200	structural constituent of cytoskeleton	0.0129946289266619
GO:0016323	basolateral plasma membrane	0.0129946289266619
GO:0007160	cell-matrix adhesion	0.0140415253671652
GO:0032403	protein complex binding	0.0140415253671652
GO:0031589	cell-substrate adhesion	0.0140415253671652
GO:0043296	apical junction complex	0.0140415253671652
GO:0016327	apicolateral plasma membrane	0.0140415253671652
GO:0008643	carbohydrate transport	0.0144805710846923
GO:0043232	intracellular non-membrane-bound organelle	0.0156300524876296
GO:0043228	non-membrane-bound organelle	0.0156300524876296
GO:0016043	cellular component organization and biogenesis	0.0183714485940823
GO:0008015	blood circulation	0.0183714485940823
GO:0003013	circulatory system process	0.0183714485940823
GO:0003012	muscle system process	0.0183714485940823
GO:0006936	muscle contraction	0.0183714485940823
GO:0005911	intercellular junction	0.0188668525064153
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0224316669169304
GO:0005886	plasma membrane	0.0225084027646801
GO:0005882	intermediate filament	0.0237728719017302
GO:0045111	intermediate filament cytoskeleton	0.0237728719017302
GO:0030036	actin cytoskeleton organization and biogenesis	0.0240114757722564
GO:0044446	intracellular organelle part	0.0240114757722564
GO:0044422	organelle part	0.0240114757722564
GO:0030029	actin filament-based process	0.0243438934286215
GO:0051239	regulation of multicellular organismal process	0.0254820419003628
GO:0015629	actin cytoskeleton	0.0266688820400185
GO:0007167	enzyme linked receptor protein signaling pathway	0.0266688820400185
GO:0030054	cell junction	0.0374397760363107
GO:0003779	actin binding	0.0376036765297134

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
classical monocyte	6.43e-07	45

Uber Anatomy

Ontology term	p-value	n
adult organism	1.10e-22	115
male reproductive organ	2.05e-08	11

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
TAL1#6886	3	22.4014625080802	0.000146275639593017	0.00188883302713342
ZBTB7A#51341	3	5.51393198090692	0.00903835282108109	0.0342224025769818

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.