Personal tools

Coexpression cluster:C3039

From FANTOM5_SSTAR

Revision as of 14:44, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3039_Pericytes_Smooth_alveolar_Fibroblast_fibrosarcoma_Lens_Meningeal



Phase1 CAGE Peaks

Hg19::chr10:71561630..71561641,+p3@COL13A1
Hg19::chr10:71561649..71561703,+p1@COL13A1
Hg19::chr10:71561704..71561747,+p2@COL13A1


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


No GOStat results

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
vasculature7.69e-3578
vascular system7.69e-3578
vessel2.11e-2868
epithelial tube open at both ends4.50e-2759
blood vessel4.50e-2759
blood vasculature4.50e-2759
vascular cord4.50e-2759
cardiovascular system5.10e-26109
splanchnic layer of lateral plate mesoderm5.69e-2683
circulatory system2.48e-25112
epithelial vesicle3.27e-2478
epithelial tube6.21e-24117
artery1.38e-2342
arterial blood vessel1.38e-2342
arterial system1.38e-2342
somite1.51e-2271
presomitic mesoderm1.51e-2271
presumptive segmental plate1.51e-2271
dermomyotome1.51e-2271
trunk paraxial mesoderm1.51e-2271
dense mesenchyme tissue5.79e-2273
paraxial mesoderm9.69e-2272
presumptive paraxial mesoderm9.69e-2272
unilaminar epithelium1.76e-21148
skeletal muscle tissue2.22e-2062
striated muscle tissue2.22e-2062
myotome2.22e-2062
muscle tissue3.25e-2064
musculature3.25e-2064
musculature of body3.25e-2064
systemic artery2.07e-1933
systemic arterial system2.07e-1933
cell layer5.66e-19309
epithelium1.14e-17306
multilaminar epithelium1.66e-1783
trunk mesenchyme8.20e-17122
mesenchyme2.13e-16160
entire embryonic mesenchyme2.13e-16160
multi-cellular organism5.69e-15656
anatomical conduit5.60e-14240
organism subdivision1.38e-13264
anatomical cluster2.91e-13373
trunk1.31e-12199
aorta1.36e-1221
aortic system1.36e-1221
anatomical system2.69e-12624
tube3.88e-12192
anatomical group4.39e-12625
multi-tissue structure1.79e-10342
mesoderm2.91e-10315
mesoderm-derived structure2.91e-10315
presumptive mesoderm2.91e-10315
simple squamous epithelium1.06e-0922
blood vessel endothelium3.84e-0918
endothelium3.84e-0918
cardiovascular system endothelium3.84e-0918
squamous epithelium2.77e-0825
embryo4.28e-08592
blood vessel smooth muscle3.59e-0710
arterial system smooth muscle3.59e-0710
artery smooth muscle tissue3.59e-0710
aorta smooth muscle tissue3.59e-0710
smooth muscle tissue5.58e-0715


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
CEBPB#105137.971147625824820.001974187055288560.0114890294142027
CTBP2#1488362.71700033932814.049570681927e-060.000128982345974313
E2F1#186934.907389214879320.008460985347239390.0323458709572215
MYC#460935.22228187160940.007020843755740150.0293124085950728
SMARCC1#6599343.66335931963151.20046018043203e-050.000300731256378366
STAT3#6774310.51946499715420.0008589184530415310.00641434281853446
TCF7L2#6934310.77017656313730.0008003181298398380.00611623190123978
TFAP2C#7022310.80922860986020.0007916746575753130.0061286568499376
ZNF263#1012738.221841637010680.001799043925565870.0108915627234464



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.