Personal tools

Coexpression cluster:C1120

From FANTOM5_SSTAR

Revision as of 13:35, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1120_adult_hairy_mycosis_B_plasma_CD4_cord



Phase1 CAGE Peaks

Hg19::chr10:69513561..69513563,-p@chr10:69513561..69513563
-
Hg19::chr5:95309942..95309984,+p@chr5:95309942..95309984
+
Hg19::chr7:142494920..142494955,+p1@TRBJ2-6
Hg19::chr8:102980193..102980205,-p@chr8:102980193..102980205
-
Hg19::chr8:102987548..102987571,-p4@NCALD
Hg19::chr8:102987581..102987599,-p5@NCALD
Hg19::chr8:103108677..103108680,-p@chr8:103108677..103108680
-


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:0030276clathrin binding0.00647592134699164
GO:0030130clathrin coat of trans-Golgi network vesicle0.00647592134699164
GO:0012510trans-Golgi network transport vesicle membrane0.00647592134699164
GO:0030125clathrin vesicle coat0.00647592134699164
GO:0030665clathrin coated vesicle membrane0.00647592134699164
GO:0030140trans-Golgi network transport vesicle0.00647592134699164
GO:0030658transport vesicle membrane0.00647592134699164
GO:0030660Golgi-associated vesicle membrane0.00647592134699164
GO:0030120vesicle coat0.0079792602311147
GO:0030662coated vesicle membrane0.0079792602311147
GO:0030133transport vesicle0.0079792602311147
GO:0030118clathrin coat0.0079792602311147
GO:0015631tubulin binding0.0079792602311147
GO:0005798Golgi-associated vesicle0.0079792602311147
GO:0030659cytoplasmic vesicle membrane0.00939008595313787
GO:0044433cytoplasmic vesicle part0.00939008595313787
GO:0012506vesicle membrane0.00939008595313787
GO:0030136clathrin-coated vesicle0.00939008595313787
GO:0030117membrane coat0.00939008595313787
GO:0048475coated membrane0.00939008595313787
GO:0030135coated vesicle0.0113328623572354
GO:0016023cytoplasmic membrane-bound vesicle0.0246219926213745
GO:0031988membrane-bound vesicle0.0246219926213745
GO:0000139Golgi membrane0.0246219926213745
GO:0044431Golgi apparatus part0.0253254781248423
GO:0031410cytoplasmic vesicle0.0253254781248423
GO:0031982vesicle0.0253254781248423
GO:0003779actin binding0.0253254781248423
GO:0005829cytosol0.031648454324814
GO:0008092cytoskeletal protein binding0.031648454324814
GO:0016192vesicle-mediated transport0.031648454324814
GO:0005794Golgi apparatus0.0351622291887437



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><br>disease_data<br>

Disease
Ontology termp-valuen
lymphoma1.00e-0910
hematologic cancer4.98e-0751
immune system cancer4.98e-0751


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
POU2F2#545245.203499461567160.003866714310179810.0190605454212899



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:C1120&oldid=2135651"