Personal tools

Coexpression cluster:C349

From FANTOM5_SSTAR

Revision as of 14:08, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C349_Mesothelial_Fibroblast_Preadipocyte_Ewing_mesenchymal_Skeletal_Smooth



Phase1 CAGE Peaks

Hg19::chr13:38138680..38138703,-p6@POSTN
Hg19::chr13:38143509..38143522,-p@chr13:38143509..38143522
-
Hg19::chr13:38143906..38143926,-p5@POSTN
Hg19::chr13:38143952..38143964,-p13@POSTN
Hg19::chr13:38144751..38144809,-p4@POSTN
Hg19::chr13:38145530..38145539,-p8@POSTN
Hg19::chr13:38145556..38145571,-p3@POSTN
Hg19::chr13:38145589..38145600,-p12@POSTN
Hg19::chr13:38148231..38148243,-p@chr13:38148231..38148243
-
Hg19::chr13:38151913..38151938,-p1@AK023481
Hg19::chr13:38153005..38153062,-p@chr13:38153005..38153062
-
Hg19::chr13:38153184..38153228,-p@chr13:38153184..38153228
-
Hg19::chr13:38153245..38153265,-p@chr13:38153245..38153265
-
Hg19::chr13:38153407..38153451,-p@chr13:38153407..38153451
-
Hg19::chr13:38153485..38153498,-p@chr13:38153485..38153498
-
Hg19::chr13:38154048..38154108,-p@chr13:38154048..38154108
-
Hg19::chr13:38154109..38154139,-p@chr13:38154109..38154139
-
Hg19::chr13:38154735..38154791,-p2@POSTN
Hg19::chr13:38154792..38154807,-p10@POSTN
Hg19::chr13:38156527..38156539,-p3@AK297914
Hg19::chr13:38156549..38156595,-p1@AK297914
Hg19::chr13:38156622..38156656,-p2@AK297914
Hg19::chr13:38158135..38158197,-p@chr13:38158135..38158197
-
Hg19::chr13:38158993..38159017,-p@chr13:38158993..38159017
-
Hg19::chr13:38160326..38160357,-p@chr13:38160326..38160357
-
Hg19::chr13:38160359..38160428,-p@chr13:38160359..38160428
-
Hg19::chr13:38161054..38161069,-p@chr13:38161054..38161069
-
Hg19::chr13:38164537..38164581,-p@chr13:38164537..38164581
-
Hg19::chr13:38164609..38164645,-p@chr13:38164609..38164645
-
Hg19::chr13:38166252..38166258,+p@chr13:38166252..38166258
+
Hg19::chr13:38171411..38171427,-p@chr13:38171411..38171427
-
Hg19::chr13:38172896..38172911,-p1@POSTN


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:0008201heparin binding0.0158880843047215
GO:0005539glycosaminoglycan binding0.0158880843047215
GO:0030247polysaccharide binding0.0158880843047215
GO:0001871pattern binding0.0158880843047215
GO:0001501skeletal development0.020917225950783
GO:0005578proteinaceous extracellular matrix0.0341709979647104
GO:0030246carbohydrate binding0.0341709979647104
GO:0044421extracellular region part0.0480395619922289
GO:0022610biological adhesion0.0480395619922289
GO:0007155cell adhesion0.0480395619922289



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue1.78e-1562
striated muscle tissue1.78e-1562
myotome1.78e-1562
muscle tissue1.24e-1464
musculature1.24e-1464
musculature of body1.24e-1464
dense mesenchyme tissue1.67e-1273
somite4.27e-1271
presomitic mesoderm4.27e-1271
presumptive segmental plate4.27e-1271
dermomyotome4.27e-1271
trunk paraxial mesoderm4.27e-1271
paraxial mesoderm8.89e-1272
presumptive paraxial mesoderm8.89e-1272
epithelial vesicle4.62e-1078
heart8.90e-1024
primitive heart tube8.90e-1024
primary heart field8.90e-1024
anterior lateral plate mesoderm8.90e-1024
heart tube8.90e-1024
heart primordium8.90e-1024
cardiac mesoderm8.90e-1024
cardiogenic plate8.90e-1024
heart rudiment8.90e-1024
artery1.70e-0942
arterial blood vessel1.70e-0942
arterial system1.70e-0942
splanchnic layer of lateral plate mesoderm2.60e-0983
multilaminar epithelium7.54e-0983
primary circulatory organ3.63e-0827
systemic artery3.18e-0733
systemic arterial system3.18e-0733
cardiovascular system9.86e-07109
Disease
Ontology termp-valuen
ovarian cancer8.87e-1114


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.