Personal tools

Coexpression cluster:C4002

From FANTOM5_SSTAR

Revision as of 11:43, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4002_Smooth_Fibroblast_Renal_Hair_spindle_Alveolar_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr1:86046433..86046453,+p1@CYR61
Hg19::chr1:86047201..86047223,+p2@CYR61
Hg19::chr1:86048263..86048315,-p@chr1:86048263..86048315
-


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
epithelial tube3.56e-25118
trunk mesenchyme1.03e-24143
trunk2.73e-23216
vasculature4.17e-2279
vascular system4.17e-2279
vessel1.03e-2069
cell layer5.02e-20312
unilaminar epithelium8.07e-20138
splanchnic layer of lateral plate mesoderm1.48e-1984
epithelium1.66e-19309
somite1.77e-1983
paraxial mesoderm1.77e-1983
presomitic mesoderm1.77e-1983
presumptive segmental plate1.77e-1983
trunk paraxial mesoderm1.77e-1983
presumptive paraxial mesoderm1.77e-1983
multilaminar epithelium2.49e-1982
organism subdivision1.73e-18365
blood vessel2.06e-1860
epithelial tube open at both ends2.06e-1860
blood vasculature2.06e-1860
vascular cord2.06e-1860
mesenchyme3.04e-18238
entire embryonic mesenchyme3.04e-18238
dermomyotome5.32e-1870
multi-cellular organism9.40e-16659
artery3.11e-1542
arterial blood vessel3.11e-1542
arterial system3.11e-1542
skeletal muscle tissue3.17e-1561
striated muscle tissue3.17e-1561
myotome3.17e-1561
multi-tissue structure3.41e-15347
muscle tissue5.54e-1563
musculature5.54e-1563
musculature of body5.54e-1563
anatomical cluster7.95e-15286
cardiovascular system2.69e-14110
circulatory system7.98e-14113
anatomical system1.15e-12625
anatomical group1.70e-12626
anatomical conduit3.90e-12241
systemic artery1.33e-1133
systemic arterial system1.33e-1133
tube4.90e-10194
subdivision of trunk1.49e-09113
mesoderm1.54e-08448
mesoderm-derived structure1.54e-08448
presumptive mesoderm1.54e-08448
organ component layer2.87e-0857
aorta9.37e-0821
aortic system9.37e-0821
surface structure1.36e-0795
integument1.43e-0745
integumental system1.43e-0745
squamous epithelium1.75e-0725
germ layer2.80e-07604
embryonic tissue2.80e-07604
presumptive structure2.80e-07604
epiblast (generic)2.80e-07604
embryonic structure3.09e-07605
developing anatomical structure3.09e-07605
embryo4.05e-07612
parenchyma4.07e-0717
immaterial anatomical entity4.66e-07126
simple squamous epithelium5.54e-0722


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
CTCF#1066435.360256373075030.0064925092527670.0279778500515652
RAD21#5885310.35503389545630.0009004912073565420.00664732832945362
TRIM28#10155212.39368336350830.008368344129438470.0329158440996695



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.