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Coexpression cluster:C2836: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.96746809587639e-06!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0109067166496056!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279911344079449
|tf_chipseq_enrich=CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.96746809587639e-06!GATA2#2624;3:9.5586988001655:0.00181815161835744:0.0109067166496056!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279911344079449
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}}
}}

Revision as of 15:45, 26 November 2012


Full id: C2836_Fibroblast_Endothelial_mature_Cardiac_Smooth_mesenchymal_Adipocyte



Phase1 CAGE Peaks

Hg19::chr6:112575490..112575527,-p3@LAMA4
Hg19::chr6:112575733..112575755,-p2@LAMA4
Hg19::chr6:112575758..112575776,-p1@LAMA4
Hg19::chr6:112575838..112575847,-p6@LAMA4


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
vasculature1.25e-2478
vascular system1.25e-2478
vessel1.40e-2168
splanchnic layer of lateral plate mesoderm1.50e-2083
epithelial tube open at both ends3.98e-1959
blood vessel3.98e-1959
blood vasculature3.98e-1959
vascular cord3.98e-1959
circulatory system2.75e-18112
cardiovascular system3.58e-18109
dense mesenchyme tissue1.44e-1773
somite2.14e-1771
presomitic mesoderm2.14e-1771
presumptive segmental plate2.14e-1771
dermomyotome2.14e-1771
trunk paraxial mesoderm2.14e-1771
paraxial mesoderm3.37e-1772
presumptive paraxial mesoderm3.37e-1772
epithelial vesicle3.62e-1778
cell layer1.65e-16309
unilaminar epithelium1.90e-16148
muscle tissue2.71e-1664
musculature2.71e-1664
musculature of body2.71e-1664
anatomical cluster4.37e-16373
anatomical conduit5.51e-16240
epithelium7.55e-16306
skeletal muscle tissue8.51e-1662
striated muscle tissue8.51e-1662
myotome8.51e-1662
epithelial tube6.49e-15117
artery8.92e-1542
arterial blood vessel8.92e-1542
arterial system8.92e-1542
multilaminar epithelium2.23e-1483
multi-cellular organism5.93e-14656
trunk mesenchyme9.72e-14122
systemic artery1.46e-1333
systemic arterial system1.46e-1333
mesenchyme3.71e-13160
entire embryonic mesenchyme3.71e-13160
anatomical system2.25e-12624
anatomical group3.93e-12625
tube8.64e-12192
multi-tissue structure1.19e-11342
organism subdivision1.06e-10264
trunk6.10e-10199
blood vessel endothelium1.65e-0918
endothelium1.65e-0918
cardiovascular system endothelium1.65e-0918
aorta3.47e-0921
aortic system3.47e-0921
squamous epithelium1.87e-0825
integument3.57e-0846
integumental system3.57e-0846
simple squamous epithelium4.86e-0822
surface structure1.49e-0799
heart4.75e-0724
primitive heart tube4.75e-0724
primary heart field4.75e-0724
anterior lateral plate mesoderm4.75e-0724
heart tube4.75e-0724
heart primordium4.75e-0724
cardiac mesoderm4.75e-0724
cardiogenic plate4.75e-0724
heart rudiment4.75e-0724
primary circulatory organ5.27e-0727


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
CTBP2#1488462.71700033932816.45042639894877e-083.96746809587639e-06
GATA2#262439.55869880016550.001818151618357440.0109067166496056
ZNF263#1012736.166381227758010.006539814347975980.0279911344079449



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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