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Coexpression cluster:C1189: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;6:4.20633361275371:0.000413523201700764:0.00393727319376662!TCF7L2#6934;5:7.69298325938382:0.000123319885015426:0.00165907580460209!ZEB1#6935;5:12.063165726817:1.38038180392597e-05:0.000333794154249189
|tf_chipseq_enrich=E2F1#1869;6:4.20633361275371:0.000413523201700764:0.00393727319376662!TCF7L2#6934;5:7.69298325938382:0.000123319885015426:0.00165907580460209!ZEB1#6935;5:12.063165726817:1.38038180392597e-05:0.000333794154249189
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}}
}}

Revision as of 14:44, 26 November 2012


Full id: C1189_Preadipocyte_Fibroblast_Ewing_mesodermal_Adipocyte_Smooth_osteoclastoma



Phase1 CAGE Peaks

Hg19::chr13:76195729..76195745,+p49@LMO7
Hg19::chr13:76209973..76210013,+p13@LMO7
Hg19::chr13:76210300..76210321,+p19@LMO7
Hg19::chr13:76210448..76210494,+p1@LMO7
Hg19::chr13:76210721..76210732,+p38@LMO7
Hg19::chr13:76210760..76210803,+p3@LMO7
Hg19::chr13:76210805..76210826,+p17@LMO7


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
fibroblast6.62e-2876
skin fibroblast3.02e-1323
multi fate stem cell2.71e-11427
somatic stem cell6.76e-11433
non-terminally differentiated cell8.54e-11106
stem cell5.92e-10441
preadipocyte3.16e-0912
somatic cell4.47e-09588
animal cell1.21e-08679
eukaryotic cell1.21e-08679
muscle precursor cell9.12e-0858
myoblast9.12e-0858
multi-potent skeletal muscle stem cell9.12e-0858
smooth muscle cell1.93e-0743
smooth muscle myoblast1.93e-0743
osteoblast6.14e-0711
osteoprogenitor cell6.14e-0711
mesenchyme condensation cell6.14e-0711
connective tissue cell6.84e-07361
motile cell7.23e-07386
Uber Anatomy
Ontology termp-valuen
surface structure1.24e-0999
skin of body3.36e-0941
integument6.30e-0946
integumental system6.30e-0946
connective tissue2.43e-07371
omentum4.14e-076
peritoneum4.14e-076
abdominal cavity4.14e-076
visceral peritoneum4.14e-076


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
E2F1#186964.206333612753710.0004135232017007640.00393727319376662
TCF7L2#693457.692983259383820.0001233198850154260.00165907580460209
ZEB1#6935512.0631657268171.38038180392597e-050.000333794154249189



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.