Personal tools

Coexpression cluster:C1278

From FANTOM5_SSTAR

Revision as of 12:43, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1278_Smooth_Endothelial_osteosarcoma_schwannoma_large_Renal_Lymphatic



Phase1 CAGE Peaks

Hg19::chr5:54274654..54274657,-p@chr5:54274654..54274657
-
Hg19::chr5:54274696..54274727,-p@chr5:54274696..54274727
-
Hg19::chr5:54275165..54275184,-p@chr5:54275165..54275184
-
Hg19::chr5:54281153..54281165,-p1@AB590689
Hg19::chr5:54281407..54281429,-p1@ESM1
Hg19::chr5:54281512..54281517,-p4@ESM1
Hg19::chr5:54281535..54281547,-p2@ESM1


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:0005520insulin-like growth factor binding0.0192020879940343
GO:0019838growth factor binding0.0192020879940343
GO:0001558regulation of cell growth0.0192020879940343
GO:0016049cell growth0.0192020879940343
GO:0040008regulation of growth0.0192020879940343
GO:0008361regulation of cell size0.0192020879940343
GO:0008083growth factor activity0.0202141259188239
GO:0000902cell morphogenesis0.0297042008451404
GO:0032989cellular structure morphogenesis0.0297042008451404
GO:0065008regulation of biological quality0.0487975391498881
GO:0005102receptor binding0.0487975391498881
GO:0009653anatomical structure morphogenesis0.0487975391498881



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
vessel1.71e-3569
vasculature2.29e-3479
vascular system2.29e-3479
blood vessel2.33e-3460
epithelial tube open at both ends2.33e-3460
blood vasculature2.33e-3460
vascular cord2.33e-3460
splanchnic layer of lateral plate mesoderm1.01e-3384
circulatory system5.40e-30113
cardiovascular system6.88e-30110
artery3.00e-2842
arterial blood vessel3.00e-2842
arterial system3.00e-2842
epithelial tube7.59e-26118
systemic artery1.11e-2233
systemic arterial system1.11e-2233
unilaminar epithelium2.92e-20138
anatomical cluster2.98e-20286
anatomical conduit8.07e-19241
skeletal muscle tissue3.70e-1661
striated muscle tissue3.70e-1661
myotome3.70e-1661
muscle tissue8.36e-1663
musculature8.36e-1663
musculature of body8.36e-1663
tube1.01e-15194
cell layer1.79e-15312
epithelium1.54e-14309
endothelium1.96e-1418
blood vessel endothelium1.96e-1418
cardiovascular system endothelium1.96e-1418
somite2.91e-1483
paraxial mesoderm2.91e-1483
presomitic mesoderm2.91e-1483
presumptive segmental plate2.91e-1483
trunk paraxial mesoderm2.91e-1483
presumptive paraxial mesoderm2.91e-1483
aorta3.51e-1421
aortic system3.51e-1421
dermomyotome5.27e-1470
simple squamous epithelium6.63e-1322
squamous epithelium9.08e-1325
multilaminar epithelium3.29e-1282
trunk mesenchyme9.63e-12143
trunk1.45e-09216
organism subdivision8.74e-09365
endothelial tube3.44e-089
arterial system endothelium3.44e-089
endothelium of artery3.44e-089
blood vessel smooth muscle6.38e-0810
arterial system smooth muscle6.38e-0810
artery smooth muscle tissue6.38e-0810
aorta smooth muscle tissue6.38e-0810
multi-tissue structure7.00e-08347
anatomical system9.74e-08625
anatomical group1.33e-07626
multi-cellular organism2.60e-07659
mesenchyme3.77e-07238
entire embryonic mesenchyme3.77e-07238
primary circulatory organ5.99e-0727
heart6.76e-0724
primitive heart tube6.76e-0724
primary heart field6.76e-0724
anterior lateral plate mesoderm6.76e-0724
heart tube6.76e-0724
heart primordium6.76e-0724
cardiac mesoderm6.76e-0724
cardiogenic plate6.76e-0724
heart rudiment6.76e-0724


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
GATA2#262435.462113600094570.01328368362592780.0469805158892067
JUN#372535.362641082429860.01397261085589020.0490565604994896
MAX#414943.68717457657550.01360570643953340.048016976137547
POLR2A#543072.147453176558070.004747636447610280.0223592353423507
STAT3#677446.011122855516710.002255779156394480.0128115351196195



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.