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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4001_Fibroblast_Smooth_mesenchymal_Mesenchymal_mesothelioma_thyroid_leiomyoma
|full_id=C4001_Fibroblast_Smooth_mesenchymal_Mesenchymal_mesothelioma_thyroid_leiomyoma
|id=C4001
|id=C4001

Revision as of 17:02, 12 September 2012


Full id: C4001_Fibroblast_Smooth_mesenchymal_Mesenchymal_mesothelioma_thyroid_leiomyoma



Phase1 CAGE Peaks

Hg19::chr1:86044170..86044182,-p12@DDAH1
Hg19::chr1:98409165..98409171,+p@chr1:98409165..98409171
+
Hg19::chr6:57127802..57127808,-p@chr6:57127802..57127808
-


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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell9.52e-42180
mesodermal cell2.30e-30119
muscle precursor cell2.50e-2357
myoblast2.50e-2357
multi-potent skeletal muscle stem cell2.50e-2357
fibroblast3.55e-2275
muscle cell6.23e-2254
contractile cell8.17e-2159
smooth muscle cell4.02e-2042
smooth muscle myoblast4.02e-2042
vascular associated smooth muscle cell9.76e-2032
electrically responsive cell2.73e-1860
electrically active cell2.73e-1860
somatic cell1.20e-16591
animal cell1.32e-13679
eukaryotic cell1.32e-13679
embryonic cell2.35e-13248
multi fate stem cell2.53e-11430
skin fibroblast1.76e-1023
somatic stem cell2.30e-10436
lining cell2.71e-0957
barrier cell2.71e-0957
stem cell3.61e-09444
meso-epithelial cell1.93e-0844
cardiocyte5.33e-0816
endothelial cell of vascular tree1.28e-0724
endothelial cell1.34e-0735
native cell1.68e-07722
aortic smooth muscle cell6.76e-0710
Uber Anatomy
Ontology termp-valuen
vasculature1.17e-2979
vascular system1.17e-2979
vessel8.95e-2769
somite1.85e-2683
paraxial mesoderm1.85e-2683
presomitic mesoderm1.85e-2683
presumptive segmental plate1.85e-2683
trunk paraxial mesoderm1.85e-2683
presumptive paraxial mesoderm1.85e-2683
splanchnic layer of lateral plate mesoderm7.90e-2684
blood vessel9.87e-2660
epithelial tube open at both ends9.87e-2660
blood vasculature9.87e-2660
vascular cord9.87e-2660
dermomyotome4.46e-2470
artery1.95e-2342
arterial blood vessel1.95e-2342
arterial system1.95e-2342
cardiovascular system3.43e-23110
epithelial tube3.26e-22118
circulatory system1.20e-21113
trunk mesenchyme1.54e-20143
skeletal muscle tissue3.28e-2061
striated muscle tissue3.28e-2061
myotome3.28e-2061
muscle tissue4.54e-2063
musculature4.54e-2063
musculature of body4.54e-2063
multilaminar epithelium5.96e-2082
unilaminar epithelium2.27e-19138
systemic artery1.87e-1833
systemic arterial system1.87e-1833
trunk3.96e-13216
cell layer6.08e-13312
epithelium2.23e-12309
aorta1.40e-1021
aortic system1.40e-1021
anatomical cluster1.45e-10286
organism subdivision2.41e-10365
integument4.28e-0945
integumental system4.28e-0945
mesenchyme9.68e-09238
entire embryonic mesenchyme9.68e-09238
skin of body3.64e-0840
mesoderm5.23e-08448
mesoderm-derived structure5.23e-08448
presumptive mesoderm5.23e-08448
tube6.63e-08194
anatomical conduit8.60e-08241
smooth muscle tissue5.91e-0715
surface structure6.28e-0795
blood vessel smooth muscle6.76e-0710
arterial system smooth muscle6.76e-0710
artery smooth muscle tissue6.76e-0710
aorta smooth muscle tissue6.76e-0710
multi-cellular organism7.06e-07659
multi-tissue structure7.93e-07347
Disease
Ontology termp-valuen
ovarian cancer1.82e-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

No analysis results for this cluster

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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