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Coexpression cluster:C2580: Difference between revisions

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|tf_chipseq_enrich=PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444160156120412!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508210812621449
|tf_chipseq_enrich=PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444160156120412!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00508210812621449
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}}
}}

Revision as of 15:35, 26 November 2012


Full id: C2580_Fibroblast_Preadipocyte_Pericytes_Adipocyte_Hair_Ewing_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:32169580..32169599,-p2@COL16A1
Hg19::chr1:32169602..32169625,-p1@COL16A1
Hg19::chr1:32169648..32169659,-p6@COL16A1
Hg19::chr1:32169676..32169690,-p4@COL16A1


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>


Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue1.77e-2273
paraxial mesoderm4.61e-2272
presumptive paraxial mesoderm4.61e-2272
somite4.97e-2271
presomitic mesoderm4.97e-2271
presumptive segmental plate4.97e-2271
dermomyotome4.97e-2271
trunk paraxial mesoderm4.97e-2271
multilaminar epithelium1.18e-2183
muscle tissue5.99e-2064
musculature5.99e-2064
musculature of body5.99e-2064
skeletal muscle tissue1.12e-1962
striated muscle tissue1.12e-1962
myotome1.12e-1962
epithelial vesicle5.43e-1978
multi-tissue structure2.52e-17342
multi-cellular organism2.45e-16656
surface structure8.42e-1699
trunk mesenchyme1.12e-13122
mesenchyme3.82e-13160
entire embryonic mesenchyme3.82e-13160
organism subdivision4.08e-13264
tissue2.30e-12773
cell layer5.99e-12309
embryonic structure2.36e-11564
epithelium2.74e-11306
germ layer7.74e-11560
germ layer / neural crest7.74e-11560
embryonic tissue7.74e-11560
presumptive structure7.74e-11560
germ layer / neural crest derived structure7.74e-11560
epiblast (generic)7.74e-11560
anatomical system9.11e-11624
anatomical group1.43e-10625
integument5.18e-1046
integumental system5.18e-1046
developing anatomical structure9.58e-10581
structure with developmental contribution from neural crest1.25e-09132
embryo1.87e-09592
ectoderm-derived structure2.40e-09171
ectoderm2.40e-09171
presumptive ectoderm2.40e-09171
anatomical cluster4.49e-09373
splanchnic layer of lateral plate mesoderm2.59e-0883
skin of body2.89e-0841
systemic artery3.88e-0833
systemic arterial system3.88e-0833
trunk4.58e-08199
artery8.50e-0842
arterial blood vessel8.50e-0842
arterial system8.50e-0842
unilaminar epithelium1.40e-07148
adipose tissue1.95e-0714
organ component layer4.47e-0766


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
PAX5#507946.669565531177830.0005052774169483260.00444160156120412
USF1#739146.361499277207960.0006105011399140830.00508210812621449



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.