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Coexpression cluster:C786

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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


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


GO IDGO nameFDR corrected p-value
GO:0005007fibroblast growth factor receptor activity0.0390969097527538
GO:0008543fibroblast growth factor receptor signaling pathway0.0390969097527538
GO:0033549MAP kinase phosphatase activity0.0390969097527538
GO:0017017MAP kinase tyrosine/serine/threonine phosphatase activity0.0390969097527538
GO:0000188inactivation of MAPK activity0.0390969097527538
GO:0051017actin filament bundle formation0.0390969097527538
GO:0051693actin filament capping0.0390969097527538
GO:0051016barbed-end actin filament capping0.0390969097527538
GO:0030835negative regulation of actin filament depolymerization0.0390969097527538
GO:0030834regulation of actin filament depolymerization0.0390969097527538
GO:0030042actin filament depolymerization0.0390969097527538
GO:0043407negative regulation of MAP kinase activity0.0390969097527538
GO:0007015actin filament organization0.0469476316525681
GO:0008064regulation of actin polymerization and/or depolymerization0.0469476316525681
GO:0051261protein depolymerization0.0469476316525681
GO:0030832regulation of actin filament length0.0469476316525681
GO:0032535regulation of cellular component size0.0469476316525681
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0469476316525681
GO:0051129negative regulation of cellular component organization and biogenesis0.0469476316525681
GO:0051493regulation of cytoskeleton organization and biogenesis0.0469476316525681
GO:0033043regulation of organelle organization and biogenesis0.0469476316525681
GO:0006469negative regulation of protein kinase activity0.0469476316525681
GO:0033673negative regulation of kinase activity0.0469476316525681
GO:0051348negative regulation of transferase activity0.0469476316525681
GO:0008154actin polymerization and/or depolymerization0.0469476316525681
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.0469476316525681
GO:0007254JNK cascade0.0469476316525681
GO:0031098stress-activated protein kinase signaling pathway0.0473519937482128



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>


Cell Type
Ontology termp-valuen
embryonic stem cell1.52e-165
metabolising cell2.07e-0712
endopolyploid cell2.07e-0712
parenchymal cell2.07e-0712
polyploid cell2.07e-0712
hepatocyte2.07e-0712
Uber Anatomy
Ontology termp-valuen
liver1.51e-0919
digestive gland1.51e-0919
liver bud1.51e-0919
hepatic diverticulum3.71e-0822
liver primordium3.71e-0822
gut epithelium7.53e-0854
abdomen element8.95e-0854
abdominal segment element8.95e-0854
digestive tract diverticulum8.97e-0823
epithelial sac4.24e-0725
epithelium of foregut-midgut junction4.24e-0725
anatomical boundary4.24e-0725
hepatobiliary system4.24e-0725
foregut-midgut junction4.24e-0725
septum transversum4.24e-0725
abdominal segment of trunk8.09e-0760
abdomen8.09e-0760
sac8.42e-0726


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


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOXA1#316944.432567899754180.008915816386211960.0338209700551936
HEY1#2346283.232088834484570.0003859230867685430.00377816097291149
RXRA#625636.022385141739980.01138448209217310.0417231261264158



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


This analysis result is provided for C0 - C305 clusters.