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Coexpression cluster:C2907: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2907_mesenchymal_myxofibrosarcoma_serous_Smooth_Endothelial_leiomyoma_Fibroblast
|full_id=C2907_mesenchymal_myxofibrosarcoma_serous_Smooth_Endothelial_leiomyoma_Fibroblast
|id=C2907
|id=C2907

Revision as of 15:42, 12 September 2012


Full id: C2907_mesenchymal_myxofibrosarcoma_serous_Smooth_Endothelial_leiomyoma_Fibroblast



Phase1 CAGE Peaks

Hg19::chr7:93551154..93551186,+p4@GNG11
Hg19::chr7:93551194..93551205,+p9@GNG11
Hg19::chr7:93551224..93551235,+p8@GNG11
Hg19::chr7:93551243..93551254,+p10@GNG11


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
cardiovascular system4.73e-36110
circulatory system1.64e-35113
vasculature4.85e-3479
vascular system4.85e-3479
vessel2.06e-2869
splanchnic layer of lateral plate mesoderm1.06e-2684
blood vessel3.79e-2660
epithelial tube open at both ends3.79e-2660
blood vasculature3.79e-2660
vascular cord3.79e-2660
anatomical cluster1.37e-25286
somite1.84e-2283
paraxial mesoderm1.84e-2283
presomitic mesoderm1.84e-2283
presumptive segmental plate1.84e-2283
trunk paraxial mesoderm1.84e-2283
presumptive paraxial mesoderm1.84e-2283
dermomyotome3.01e-2270
epithelial tube3.17e-22118
cell layer2.61e-21312
artery8.73e-2142
arterial blood vessel8.73e-2142
arterial system8.73e-2142
epithelium5.70e-20309
skeletal muscle tissue1.33e-1961
striated muscle tissue1.33e-1961
myotome1.33e-1961
muscle tissue2.12e-1963
musculature2.12e-1963
musculature of body2.12e-1963
anatomical conduit1.92e-18241
tube1.70e-17194
unilaminar epithelium3.23e-17138
trunk mesenchyme3.70e-17143
organism subdivision5.02e-17365
multilaminar epithelium1.73e-1682
systemic artery3.20e-1633
systemic arterial system3.20e-1633
multi-tissue structure4.99e-16347
multi-cellular organism9.02e-16659
anatomical system7.02e-15625
anatomical group1.40e-14626
trunk2.74e-12216
endothelium3.73e-1118
blood vessel endothelium3.73e-1118
cardiovascular system endothelium3.73e-1118
simple squamous epithelium4.48e-1122
embryonic structure2.77e-10605
developing anatomical structure2.77e-10605
germ layer2.96e-10604
embryonic tissue2.96e-10604
presumptive structure2.96e-10604
epiblast (generic)2.96e-10604
squamous epithelium4.51e-1025
embryo5.05e-10612
mesenchyme5.24e-10238
entire embryonic mesenchyme5.24e-10238
aorta1.45e-0921
aortic system1.45e-0921
heart3.81e-0724
primitive heart tube3.81e-0724
primary heart field3.81e-0724
anterior lateral plate mesoderm3.81e-0724
heart tube3.81e-0724
heart primordium3.81e-0724
cardiac mesoderm3.81e-0724
cardiogenic plate3.81e-0724
heart rudiment3.81e-0724
primary circulatory organ9.92e-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
CTCF#1066445.360256373075030.001211145381643620.00820090848764771
EBF1#187948.9064668465690.00015887907472010.00200183033956962
FOS#235348.99795530889440.0001525147711168630.00195513565492501
GATA2#2624412.7449317335543.78864877853583e-050.000724826323102224
NR3C1#2908414.9730233311731.98868032687801e-050.000444744720896814
RAD21#588537.766275421592250.0033411193858720.0172786911384544
REST#597849.650028716128020.0001152825614219170.00157570938782144
SMARCB1#6598418.25271578115749.00423392720929e-060.000242306927885548
TFAP2A#7020416.5186343730451.34240829060362e-050.000327493061112711
TFAP2C#7022410.80922860986027.32289634782688e-050.00114920506637219



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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