Personal tools

Coexpression cluster:C496

From FANTOM5_SSTAR

Revision as of 18:03, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C496_thymus_CD4_CD8_hairy_vein_chronic_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:3968515..3968532,+p3@STIM1
Hg19::chr14:22265490..22265505,+p4@TRAV8-1
Hg19::chr14:22320634..22320645,+p1@TRAV8-3
Hg19::chr15:22466523..22466550,-p1@uc001yui.1
Hg19::chr16:56742627..56742637,+p@chr16:56742627..56742637
+
Hg19::chr17:78717112..78717159,+p2@RPTOR
Hg19::chr2:95740646..95740655,+p@chr2:95740646..95740655
+
Hg19::chr4:40192677..40192712,+p4@RHOH
Hg19::chr6:128222238..128222249,-p5@THEMIS
Hg19::chr7:142028105..142028159,+p1@TRBV6-1
Hg19::chr7:142162390..142162425,-p1@TRBV6-6
Hg19::chr7:142180964..142180969,-p4@TRBV6-5
Hg19::chr7:142180978..142181006,-p1@TRBV6-5
Hg19::chr7:142198109..142198132,-p2@TRBV11-2
Hg19::chr7:142334728..142334737,+p1@AB306258
Hg19::chr7:142344506..142344509,+p1@AJ296363
p1@AJ296373
p1@HM236738
Hg19::chr7:142498815..142498839,+p1@AJ568018
Hg19::chr7:142507125..142507136,+p@chr7:142507125..142507136
+
Hg19::chr9:33446618..33446630,+p@chr9:33446618..33446630
+


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:0032236positive regulation of calcium ion transport via store-operated calcium channel0.00473317045069122
GO:0032237activation of store-operated calcium channel activity0.00473317045069122
GO:0043270positive regulation of ion transport0.00473317045069122
GO:0032234regulation of calcium ion transport via store-operated calcium channel0.00473317045069122
GO:0051928positive regulation of calcium ion transport0.00473317045069122
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.011831532856717
GO:0005513detection of calcium ion0.0135209557288322
GO:0005095GTPase inhibitor activity0.0147876746201048
GO:0051924regulation of calcium ion transport0.015772590875712
GO:0043269regulation of ion transport0.0193538515139206
GO:0009593detection of chemical stimulus0.0193538515139206
GO:0017048Rho GTPase binding0.0315266113806201
GO:0051050positive regulation of transport0.0330931953761501
GO:0030217T cell differentiation0.0330931953761501
GO:0019210kinase inhibitor activity0.0330931953761501
GO:0030176integral to endoplasmic reticulum membrane0.038264986352189
GO:0002376immune system process0.038264986352189
GO:0031227intrinsic to endoplasmic reticulum membrane0.0397855755213595
GO:0030098lymphocyte differentiation0.0397855755213595
GO:0017016Ras GTPase binding0.043249602836329
GO:0051606detection of stimulus0.043249602836329
GO:0031267small GTPase binding0.043249602836329
GO:0002521leukocyte differentiation0.043249602836329
GO:0051020GTPase binding0.043249602836329
GO:0009615response to virus0.043249602836329
GO:0042110T cell activation0.043249602836329
GO:0009968negative regulation of signal transduction0.043249602836329
GO:0048771tissue remodeling0.043249602836329
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.043249602836329
GO:0051049regulation of transport0.043249602836329
GO:0045087innate immune response0.0433713217382676
GO:0019207kinase regulator activity0.0449538569971292
GO:0031301integral to organelle membrane0.048180952305821
GO:0007249I-kappaB kinase/NF-kappaB cascade0.048180952305821



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>

Uber Anatomy
Ontology termp-valuen
adult organism2.93e-20115
hematopoietic system6.72e-09102
blood island6.72e-09102
blood1.54e-0815
haemolymphatic fluid1.54e-0815
organism substance1.54e-0815
hemolymphoid system1.61e-07112


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

No analysis results for this cluster

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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C496&oldid=2139840"