Coexpression cluster:C1277

Full id: C1277_Hepatocyte_mature_mesenchymal_smooth_bladder_normal_cholangiocellular

Phase1 CAGE Peaks

Hg19::chr5:52083909..52083927,+	p7@PELO
Hg19::chr5:52083929..52083940,+	p12@PELO
Hg19::chr5:52083991..52084021,+	p3@ITGA1
Hg19::chr5:52084023..52084051,+	p2@ITGA1
Hg19::chr5:52084059..52084086,+	p4@ITGA1
Hg19::chr5:52084087..52084115,+	p5@ITGA1
Hg19::chr5:52084126..52084133,+	p8@ITGA1

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:0045123	cellular extravasation	0.0155415249616414
GO:0030593	neutrophil chemotaxis	0.0223346942055352
GO:0005518	collagen binding	0.0223346942055352
GO:0030595	leukocyte chemotaxis	0.0223346942055352
GO:0050900	leukocyte migration	0.0240797902081608
GO:0009897	external side of plasma membrane	0.0305050789062747
GO:0008305	integrin complex	0.0305050789062747
GO:0007229	integrin-mediated signaling pathway	0.038793191786861
GO:0007160	cell-matrix adhesion	0.038793191786861
GO:0031589	cell-substrate adhesion	0.038793191786861
GO:0043235	receptor complex	0.038793191786861
GO:0042330	taxis	0.0409869718598991
GO:0006935	chemotaxis	0.0409869718598991
GO:0009986	cell surface	0.0409869718598991
GO:0007626	locomotory behavior	0.0467614554761341

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	3.49e-13	114
multi-tissue structure	4.99e-12	342
anatomical cluster	8.30e-11	373
multi-cellular organism	6.27e-10	656
digestive system	8.25e-10	145
digestive tract	8.25e-10	145
primitive gut	8.25e-10	145
subdivision of digestive tract	9.24e-10	118
mesenchyme	3.32e-08	160
entire embryonic mesenchyme	3.32e-08	160
endoderm-derived structure	4.05e-08	160
endoderm	4.05e-08	160
presumptive endoderm	4.05e-08	160
primordium	7.46e-08	160
liver	1.69e-07	19
digestive gland	1.69e-07	19
liver bud	1.69e-07	19
trunk mesenchyme	2.39e-07	122
organ system subdivision	2.81e-07	223
sac	4.22e-07	26
trunk	6.55e-07	199
digestive tract diverticulum	6.73e-07	23
endocrine gland	7.92e-07	35
anatomical system	9.39e-07	624

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
CEBPB#1051	7	7.97114762582482	4.88663622402061e-07	2.30200902390838e-05
CTCF#10664	7	5.36025637307503	7.86114662284756e-06	0.00022249601413105
E2F1#1869	7	4.90738921487932	1.45832274679793e-05	0.000347017018347754
E2F6#1876	7	5.01715573169739	1.24910426162553e-05	0.000308331836397799
EP300#2033	7	6.7739417262232	1.52695018318475e-06	5.86729765201002e-05
FOXA2#3170	7	24.6304637526652	1.81353313360781e-10	1.89214372568298e-08
HNF4A#3172	7	23.1322903629537	2.81434373816722e-10	2.86199849727796e-08
HNF4G#3174	7	28.7534225264468	6.13483972627905e-11	6.8379565226559e-09
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223582271250381
RAD21#5885	5	7.3964527824688	0.000149101450522837	0.00192341976175328
SMARCB1#6598	7	18.2527157811574	1.4786181847889e-09	1.31425876256313e-07
SMC3#9126	5	10.7463806035235	2.42943476743625e-05	0.000527171696813369
SP1#6667	7	5.6983813781409	5.12280185510121e-06	0.000157358912630857
SRF#6722	7	13.7971782621678	1.04914736064956e-08	7.9113286064173e-07
TAF1#6872	7	3.34304628574529	0.000214233631962245	0.00246848480676356
TFAP2C#7022	7	10.8092286098602	5.79365976833206e-08	3.61459995546495e-06
YY1#7528	7	4.91117074985386	1.45048003565243e-05	0.000345623281869732
ZNF263#10127	7	8.22184163701068	3.93423095812578e-07	1.91021453759041e-05

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.