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Coexpression cluster:C3453: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3453_Fibroblast_Smooth_Preadipocyte_aorta_Chondrocyte_spindle_mesenchymal
|full_id=C3453_Fibroblast_Smooth_Preadipocyte_aorta_Chondrocyte_spindle_mesenchymal
|id=C3453
|id=C3453

Revision as of 16:23, 12 September 2012


Full id: C3453_Fibroblast_Smooth_Preadipocyte_aorta_Chondrocyte_spindle_mesenchymal



Phase1 CAGE Peaks

Hg19::chr14:75078847..75078857,-p10@LTBP2
Hg19::chr14:75078867..75078893,-p4@LTBP2
Hg19::chr14:75078895..75078916,-p3@LTBP2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
vasculature4.83e-2479
vascular system4.83e-2479
splanchnic layer of lateral plate mesoderm7.87e-2384
blood vessel1.51e-2060
epithelial tube open at both ends1.51e-2060
blood vasculature1.51e-2060
vascular cord1.51e-2060
vessel2.10e-2069
circulatory system1.11e-18113
cardiovascular system3.80e-18110
epithelial tube9.90e-18118
somite1.14e-1783
paraxial mesoderm1.14e-1783
presomitic mesoderm1.14e-1783
presumptive segmental plate1.14e-1783
trunk paraxial mesoderm1.14e-1783
presumptive paraxial mesoderm1.14e-1783
artery1.45e-1742
arterial blood vessel1.45e-1742
arterial system1.45e-1742
multilaminar epithelium1.09e-1682
multi-cellular organism4.32e-16659
dermomyotome1.43e-1570
skeletal muscle tissue1.26e-1461
striated muscle tissue1.26e-1461
myotome1.26e-1461
cell layer1.34e-14312
organism subdivision1.83e-14365
muscle tissue1.99e-1463
musculature1.99e-1463
musculature of body1.99e-1463
epithelium4.02e-14309
systemic artery5.33e-1433
systemic arterial system5.33e-1433
trunk mesenchyme1.32e-13143
anatomical system1.42e-13625
anatomical group2.51e-13626
unilaminar epithelium9.66e-12138
trunk1.83e-11216
surface structure4.75e-1195
anatomical cluster6.42e-11286
anatomical conduit2.65e-10241
aorta5.54e-1021
aortic system5.54e-1021
multi-tissue structure2.69e-08347
integument6.30e-0845
integumental system6.30e-0845
primary circulatory organ7.78e-0827
tube1.77e-07194
heart2.07e-0724
primitive heart tube2.07e-0724
primary heart field2.07e-0724
anterior lateral plate mesoderm2.07e-0724
heart tube2.07e-0724
heart primordium2.07e-0724
cardiac mesoderm2.07e-0724
cardiogenic plate2.07e-0724
heart rudiment2.07e-0724
embryonic structure3.57e-07605
developing anatomical structure3.57e-07605
embryo3.61e-07612
mesoderm4.04e-07448
mesoderm-derived structure4.04e-07448
presumptive mesoderm4.04e-07448
germ layer5.08e-07604
embryonic tissue5.08e-07604
presumptive structure5.08e-07604
epiblast (generic)5.08e-07604
tissue7.46e-07787
mesenchyme7.93e-07238
entire embryonic mesenchyme7.93e-07238
Disease
Ontology termp-valuen
ovarian cancer9.32e-0714


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
E2F6#187635.017155731697390.00791769806886330.0321307300518345



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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