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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2257_gastric_Fibroblast_synovial_alveolar_osteosarcoma_Smooth_mesenchymal
|full_id=C2257_gastric_Fibroblast_synovial_alveolar_osteosarcoma_Smooth_mesenchymal
|id=C2257
|id=C2257

Revision as of 14:57, 12 September 2012


Full id: C2257_gastric_Fibroblast_synovial_alveolar_osteosarcoma_Smooth_mesenchymal



Phase1 CAGE Peaks

Hg19::chr13:24153488..24153553,+p1@TNFRSF19
Hg19::chr13:24153554..24153576,+p4@TNFRSF19
Hg19::chr13:24153584..24153602,+p5@TNFRSF19
Hg19::chr13:24153617..24153622,+p11@TNFRSF19


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.60e-24180
fibroblast2.36e-1375
skin fibroblast1.76e-0823
Uber Anatomy
Ontology termp-valuen
organism subdivision1.06e-21365
multi-tissue structure2.37e-17347
surface structure1.00e-1195
trunk mesenchyme1.69e-10143
somite2.24e-1083
paraxial mesoderm2.24e-1083
presomitic mesoderm2.24e-1083
presumptive segmental plate2.24e-1083
trunk paraxial mesoderm2.24e-1083
presumptive paraxial mesoderm2.24e-1083
trunk5.50e-09216
cell layer6.63e-09312
mesenchyme7.28e-09238
entire embryonic mesenchyme7.28e-09238
epithelium1.55e-08309
organ6.74e-08511
dermomyotome9.99e-0870
head1.23e-07123
anterior region of body1.46e-07129
craniocervical region1.46e-07129
integument2.13e-0745
integumental system2.13e-0745
multi-cellular organism2.91e-07659
skin of body2.96e-0740
anatomical system7.51e-07625
anatomical group8.66e-07626


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
CHD2#1106410.34402283411698.73193255208051e-050.0012895281445231
EGR1#195844.988179094810140.001615011500076050.0101315585089166
HEY1#2346244.040111043105710.00375304636917980.0185685920579265
IRF1#365947.63716375356390.0002938853996185490.00307023079431446
SIN3A#2594245.408884726815140.001168172384885160.00794961593177955
TAF1#687243.343046285745290.008005664898701650.0321528855697393



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.