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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C908_Mesothelial_mesenchymal_squamous_mesothelioma_mucinous_oral_Smooth
|full_id=C908_Mesothelial_mesenchymal_squamous_mesothelioma_mucinous_oral_Smooth
|id=C908
|id=C908

Revision as of 18:41, 12 September 2012


Full id: C908_Mesothelial_mesenchymal_squamous_mesothelioma_mucinous_oral_Smooth



Phase1 CAGE Peaks

Hg19::chr15:101420028..101420044,+p1@ALDH1A3
Hg19::chr15:101434235..101434249,+p@chr15:101434235..101434249
+
Hg19::chr15:101438349..101438359,+p2@ALDH1A3
Hg19::chr15:101440861..101440879,+p@chr15:101440861..101440879
+
Hg19::chr15:101445823..101445841,+p@chr15:101445823..101445841
+
Hg19::chr15:101448609..101448622,+p@chr15:101448609..101448622
+
Hg19::chr15:101455085..101455101,+p@chr15:101455085..101455101
+
Hg19::chr15:101455401..101455413,+p@chr15:101455401..101455413
+
Hg19::chr15:101455438..101455471,+p@chr15:101455438..101455471
+


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
organism subdivision6.14e-23365
multi-tissue structure7.95e-23347
cell layer1.33e-18312
epithelium1.64e-18309
mesenchyme8.79e-18238
entire embryonic mesenchyme8.79e-18238
trunk1.26e-16216
multi-cellular organism1.83e-16659
anatomical system7.43e-16625
anatomical group1.52e-15626
anatomical conduit1.66e-15241
anatomical cluster5.71e-15286
multilaminar epithelium1.23e-1482
trunk mesenchyme2.10e-14143
artery1.74e-1342
arterial blood vessel1.74e-1342
arterial system1.74e-1342
epithelial tube3.37e-13118
primordium8.00e-13168
embryo1.01e-12612
embryonic structure3.82e-12605
developing anatomical structure3.82e-12605
germ layer6.98e-12604
embryonic tissue6.98e-12604
presumptive structure6.98e-12604
epiblast (generic)6.98e-12604
splanchnic layer of lateral plate mesoderm9.56e-1284
muscle tissue1.72e-1163
musculature1.72e-1163
musculature of body1.72e-1163
skeletal muscle tissue2.54e-1161
striated muscle tissue2.54e-1161
myotome2.54e-1161
unilaminar epithelium2.58e-11138
endoderm-derived structure2.77e-11169
endoderm2.77e-11169
presumptive endoderm2.77e-11169
dermomyotome8.58e-1170
systemic artery9.92e-1133
systemic arterial system9.92e-1133
surface structure1.17e-1095
anatomical space1.61e-10104
blood vessel3.49e-1060
epithelial tube open at both ends3.49e-1060
blood vasculature3.49e-1060
vascular cord3.49e-1060
somite3.58e-1083
paraxial mesoderm3.58e-1083
presomitic mesoderm3.58e-1083
presumptive segmental plate3.58e-1083
trunk paraxial mesoderm3.58e-1083
presumptive paraxial mesoderm3.58e-1083
vessel1.52e-0969
digestive system2.04e-09155
digestive tract2.04e-09155
primitive gut2.04e-09155
vasculature3.26e-0979
vascular system3.26e-0979
immaterial anatomical entity4.19e-09126
tube4.49e-09194
anatomical cavity4.89e-0970
body cavity precursor6.99e-0963
body cavity or lining1.77e-0849
body cavity1.08e-0746
subdivision of digestive tract1.90e-07129
endodermal part of digestive tract1.90e-07129
reproductive structure1.96e-0759
reproductive system1.96e-0759
compound organ2.29e-0769
orifice2.34e-0735
organ part4.12e-07219
organ8.81e-07511
Disease
Ontology termp-valuen
ovarian cancer3.89e-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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