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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2386_mesothelioma_Mast_pons_mature_endometrial_Mesothelial_medulla
|full_id=C2386_mesothelioma_Mast_pons_mature_endometrial_Mesothelial_medulla
|id=C2386
|id=C2386

Revision as of 15:06, 12 September 2012


Full id: C2386_mesothelioma_Mast_pons_mature_endometrial_Mesothelial_medulla



Phase1 CAGE Peaks

Hg19::chr16:71392619..71392635,+p1@CALB2
Hg19::chr16:71417294..71417313,+p@chr16:71417294..71417313
+
Hg19::chr16:71423775..71423790,+p@chr16:71423775..71423790
+
Hg19::chr16:71423847..71423869,+p@chr16:71423847..71423869
+


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism5.92e-23115
central nervous system3.85e-2282
neural tube8.80e-2257
neural rod8.80e-2257
future spinal cord8.80e-2257
neural keel8.80e-2257
regional part of nervous system6.78e-2094
nervous system6.78e-2094
regional part of brain2.92e-1859
brain3.34e-1869
future brain3.34e-1869
tube3.78e-17194
neural plate8.63e-1786
presumptive neural plate8.63e-1786
anterior neural tube7.04e-1642
organism subdivision2.60e-15365
regional part of forebrain2.73e-1541
forebrain2.73e-1541
future forebrain2.73e-1541
anatomical conduit2.96e-15241
neurectoderm1.56e-1490
gray matter3.81e-1434
brain grey matter3.81e-1434
ectoderm-derived structure7.25e-14169
telencephalon1.02e-1334
cerebral hemisphere1.97e-1332
regional part of telencephalon3.12e-1333
anatomical cluster1.27e-12286
multi-tissue structure1.65e-12347
ectoderm1.71e-12173
presumptive ectoderm1.71e-12173
regional part of cerebral cortex3.35e-1222
organ2.39e-11511
neocortex3.08e-1120
pre-chordal neural plate5.31e-1161
head1.38e-10123
anterior region of body1.83e-10129
craniocervical region1.83e-10129
cerebral cortex2.08e-1025
pallium2.08e-1025
epithelium3.68e-09309
multi-cellular organism1.08e-08659
cell layer1.52e-08312
anatomical system2.36e-08625
anatomical group3.58e-08626
primordium8.25e-08168
body cavity8.81e-0846
organ part1.80e-07219
body cavity or lining2.66e-0749
embryo2.70e-07612
posterior neural tube3.73e-0715
chordal neural plate3.73e-0715
Disease
Ontology termp-valuen
ovarian cancer5.41e-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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