Coexpression cluster:C786

Full id: C786_liver_hepatocellular_placenta_hepatoblastoma_normal_Intestinal_Wilms

Phase1 CAGE Peaks

Hg19::chr10:72083650..72083662,-	p7@LRRC20
Hg19::chr5:176514428..176514437,+	p7@FGFR4
Hg19::chr8:21911054..21911086,+	p9@EPB49
Hg19::chr8:21911140..21911149,+	p40@EPB49
Hg19::chrX:132887732..132887744,-	p9@GPC3
Hg19::chrX:133119565..133119581,-	p4@GPC3
Hg19::chrX:133119584..133119595,-	p5@GPC3
Hg19::chrX:133119601..133119627,-	p1@GPC3
Hg19::chrX:152907882..152907906,+	p2@DUSP9
Hg19::chrX:152911654..152911663,+	p@chrX:152911654..152911663 +

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:0005007	fibroblast growth factor receptor activity	0.0390969097527538
GO:0008543	fibroblast growth factor receptor signaling pathway	0.0390969097527538
GO:0033549	MAP kinase phosphatase activity	0.0390969097527538
GO:0017017	MAP kinase tyrosine/serine/threonine phosphatase activity	0.0390969097527538
GO:0000188	inactivation of MAPK activity	0.0390969097527538
GO:0051017	actin filament bundle formation	0.0390969097527538
GO:0051693	actin filament capping	0.0390969097527538
GO:0051016	barbed-end actin filament capping	0.0390969097527538
GO:0030835	negative regulation of actin filament depolymerization	0.0390969097527538
GO:0030834	regulation of actin filament depolymerization	0.0390969097527538
GO:0030042	actin filament depolymerization	0.0390969097527538
GO:0043407	negative regulation of MAP kinase activity	0.0390969097527538
GO:0007015	actin filament organization	0.0469476316525681
GO:0008064	regulation of actin polymerization and/or depolymerization	0.0469476316525681
GO:0051261	protein depolymerization	0.0469476316525681
GO:0030832	regulation of actin filament length	0.0469476316525681
GO:0032535	regulation of cellular component size	0.0469476316525681
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.0469476316525681
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0469476316525681
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.0469476316525681
GO:0033043	regulation of organelle organization and biogenesis	0.0469476316525681
GO:0006469	negative regulation of protein kinase activity	0.0469476316525681
GO:0033673	negative regulation of kinase activity	0.0469476316525681
GO:0051348	negative regulation of transferase activity	0.0469476316525681
GO:0008154	actin polymerization and/or depolymerization	0.0469476316525681
GO:0008138	protein tyrosine/serine/threonine phosphatase activity	0.0469476316525681
GO:0007254	JNK cascade	0.0469476316525681
GO:0031098	stress-activated protein kinase signaling pathway	0.0473519937482128

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
embryonic stem cell	1.52e-16	5
metabolising cell	2.07e-07	12
endopolyploid cell	2.07e-07	12
parenchymal cell	2.07e-07	12
polyploid cell	2.07e-07	12
hepatocyte	2.07e-07	12

Uber Anatomy

Ontology term	p-value	n
liver	1.51e-09	19
digestive gland	1.51e-09	19
liver bud	1.51e-09	19
hepatic diverticulum	3.71e-08	22
liver primordium	3.71e-08	22
gut epithelium	7.53e-08	54
abdomen element	8.95e-08	54
abdominal segment element	8.95e-08	54
digestive tract diverticulum	8.97e-08	23
epithelial sac	4.24e-07	25
epithelium of foregut-midgut junction	4.24e-07	25
anatomical boundary	4.24e-07	25
hepatobiliary system	4.24e-07	25
foregut-midgut junction	4.24e-07	25
septum transversum	4.24e-07	25
abdominal segment of trunk	8.09e-07	60
abdomen	8.09e-07	60
sac	8.42e-07	26

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
FOXA1#3169	4	4.43256789975418	0.00891581638621196	0.0338209700551936
HEY1#23462	8	3.23208883448457	0.000385923086768543	0.00377816097291149
RXRA#6256	3	6.02238514173998	0.0113844820921731	0.0417231261264158

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.