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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2021_basal_mesenchymal_Dendritic_Smooth_Fibroblast_Aortic_Mallassezderived
|full_id=C2021_basal_mesenchymal_Dendritic_Smooth_Fibroblast_Aortic_Mallassezderived
|id=C2021
|id=C2021

Revision as of 14:41, 12 September 2012


Full id: C2021_basal_mesenchymal_Dendritic_Smooth_Fibroblast_Aortic_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr9:5510492..5510552,+p1@PDCD1LG2
Hg19::chr9:5510558..5510567,+p2@PDCD1LG2
Hg19::chr9:5510574..5510587,+p3@PDCD1LG2
Hg19::chr9:5510607..5510612,+p5@PDCD1LG2
Hg19::chr9:5510613..5510622,+p4@PDCD1LG2


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
splanchnic layer of lateral plate mesoderm2.77e-1984
vessel2.12e-1769
vasculature2.18e-1679
vascular system2.18e-1679
blood vessel4.03e-1660
epithelial tube open at both ends4.03e-1660
blood vasculature4.03e-1660
vascular cord4.03e-1660
somite4.81e-1683
paraxial mesoderm4.81e-1683
presomitic mesoderm4.81e-1683
presumptive segmental plate4.81e-1683
trunk paraxial mesoderm4.81e-1683
presumptive paraxial mesoderm4.81e-1683
artery9.01e-1642
arterial blood vessel9.01e-1642
arterial system9.01e-1642
lateral plate mesoderm1.62e-15216
multilaminar epithelium4.48e-1582
cardiovascular system1.62e-14110
circulatory system7.34e-14113
dermomyotome7.88e-1470
musculoskeletal system8.17e-14167
systemic artery4.77e-1333
systemic arterial system4.77e-1333
skeletal muscle tissue5.54e-1261
striated muscle tissue5.54e-1261
myotome5.54e-1261
muscle tissue1.12e-1163
musculature1.12e-1163
musculature of body1.12e-1163
anatomical group3.92e-10626
anatomical system4.41e-10625
epithelial tube9.32e-10118
trunk mesenchyme3.50e-09143
unilaminar epithelium8.77e-09138
aorta1.56e-0821
aortic system1.56e-0821
mesoderm3.53e-08448
mesoderm-derived structure3.53e-08448
presumptive mesoderm3.53e-08448
multi-cellular organism5.16e-08659
surface structure7.29e-0895
integument7.74e-0845
integumental system7.74e-0845
skin of body1.34e-0740
blood vessel smooth muscle4.39e-0710
arterial system smooth muscle4.39e-0710
artery smooth muscle tissue4.39e-0710
aorta smooth muscle tissue4.39e-0710


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
BATF#10538524.35780179230361.16482472299935e-076.74726174405599e-06
BCL11A#53335528.36945510360715.43377642717329e-083.44564770053158e-06
IRF4#3662521.91451268674411.97628413609567e-071.07444632425661e-05
JUND#372756.994663941871035.97069468343598e-050.000985886770029043
NFKB1#479055.488063424193840.0002008162847462320.00239363752141197
PAX5#507956.669565531177837.57493746384605e-050.00117202799079499
REST#597859.650028716128021.19441074361324e-050.000301822075132405
SP1#666755.69838137814090.000166391843712550.00204589095426124
SPI1#668858.204323508522732.68916109982495e-050.000575991173307256
SRF#6722513.79717826216781.9987012616697e-067.32943683523602e-05
STAT3#6774510.51946499715427.759040745861e-060.000220863029832918
TAF1#687253.343046285745290.002394600090870310.0135594035399265



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.

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