Personal tools

Coexpression cluster:C889

From FANTOM5_SSTAR

Revision as of 09:39, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C889_mesothelioma_mesodermal_lung_placenta_umbilical_Urothelial_Mallassezderived



Phase1 CAGE Peaks

  Short description
Hg19::chr12:106477805..106477824,- p13@NUAK1
Hg19::chr12:80175910..80175928,- p31@PPP1R12A
Hg19::chr17:26890530..26890545,- p@chr17:26890530..26890545
-
Hg19::chr17:26890583..26890593,- p@chr17:26890583..26890593
-
Hg19::chr17:67586124..67586131,+ p1@uc002jil.2
Hg19::chr3:129023260..129023267,+ p3@AF035296
Hg19::chr4:23022304..23022336,+ p@chr4:23022304..23022336
+
Hg19::chr8:141728444..141728461,- p23@PTK2
Hg19::chr8:141728472..141728496,- p19@PTK2


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


p.valueFDRnGenesnPathwayName
0.0001458532098643570.02642575022000882200Focal adhesion (KEGG):04510
0.0001669873631596130.02642575022000882214Regulation of actin cytoskeleton (KEGG):04810
0.0001288708350416320.02642575022000882188Focal Adhesion (Wikipathways):WP306
7.66167144514812e-050.02642575022000882145Regulation of Actin Cytoskeleton (Wikipathways):WP51



Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0007172signal complex assembly0.0300359574741371
GO:0042169SH2 domain binding0.0300359574741371
GO:0005925focal adhesion0.0300359574741371
GO:0005924cell-substrate adherens junction0.0300359574741371
GO:0004672protein kinase activity0.0300359574741371
GO:0006937regulation of muscle contraction0.0300359574741371
GO:0006468protein amino acid phosphorylation0.0300359574741371
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0300359574741371
GO:0030055cell-matrix junction0.0300359574741371
GO:0005912adherens junction0.0300359574741371
GO:0016310phosphorylation0.0300359574741371
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0300359574741371
GO:0005856cytoskeleton0.0300359574741371
GO:0043623cellular protein complex assembly0.030700721916763
GO:0016301kinase activity0.030700721916763
GO:0006793phosphorus metabolic process0.030700721916763
GO:0006796phosphate metabolic process0.030700721916763
GO:0016323basolateral plasma membrane0.030700721916763
GO:0007229integrin-mediated signaling pathway0.030700721916763
GO:0016772transferase activity, transferring phosphorus-containing groups0.0369879296170742
GO:0019904protein domain specific binding0.0409697638742895
GO:0043687post-translational protein modification0.0434369027088801
GO:0003012muscle system process0.0465227350691899
GO:0006936muscle contraction0.0465227350691899
GO:0006464protein modification process0.0492255124386033
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0492255124386033
GO:0005515protein binding0.0492255124386033
GO:0005524ATP binding0.0492255124386033
GO:0043412biopolymer modification0.0492255124386033
GO:0032559adenyl ribonucleotide binding0.0492255124386033
GO:0043232intracellular non-membrane-bound organelle0.0492255124386033
GO:0043228non-membrane-bound organelle0.0492255124386033
GO:0030554adenyl nucleotide binding0.0492255124386033



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism2.97e-08115


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.