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Coexpression cluster:C3169: Difference between revisions

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|tf_chipseq_enrich=FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000370140969217304!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242353305554394!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185827019283323!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293264768630063!REST#5978;3:9.65002871612802:0.00111263624711459:0.00765447711036168
|tf_chipseq_enrich=FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000370140969217304!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242353305554394!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185827019283323!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293264768630063!REST#5978;3:9.65002871612802:0.00111263624711459:0.00765447711036168
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}}
}}

Revision as of 15:58, 26 November 2012


Full id: C3169_Nucleus_Fibroblast_pagetoid_Pericytes_Anulus_Mesenchymal_Skeletal



Phase1 CAGE Peaks

Hg19::chr11:60640829..60640871,+p@chr11:60640829..60640871
+
Hg19::chr11:60640875..60640891,+p@chr11:60640875..60640891
+
Hg19::chr11:60640905..60640919,+p@chr11:60640905..60640919
+


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
muscle tissue1.61e-1764
musculature1.61e-1764
musculature of body1.61e-1764
skeletal muscle tissue2.95e-1762
striated muscle tissue2.95e-1762
myotome2.95e-1762
somite3.61e-1671
presomitic mesoderm3.61e-1671
presumptive segmental plate3.61e-1671
dermomyotome3.61e-1671
trunk paraxial mesoderm3.61e-1671
paraxial mesoderm8.41e-1672
presumptive paraxial mesoderm8.41e-1672
dense mesenchyme tissue1.91e-1573
epithelial vesicle8.19e-1478
multilaminar epithelium2.16e-1283
mesenchyme6.76e-12160
entire embryonic mesenchyme6.76e-12160
trunk mesenchyme3.58e-11122
intervertebral cartilage8.82e-105
symphysis8.82e-105
nonsynovial joint8.82e-105
fibrous joint8.82e-105
cartilaginous joint8.82e-105
developing mesenchymal condensation8.82e-105
pre-cartilage condensation8.82e-105
cartilaginous condensation8.82e-105
cartilage element8.82e-105
post-cranial axial skeletal system8.82e-105
vertebral column8.82e-105
intervertebral disk8.82e-105
intervertebral joint8.82e-105
brain vasculature1.74e-095
unilaminar epithelium3.32e-09148
vasculature of organ9.44e-0911
smooth muscle tissue4.69e-0715
Disease
Ontology termp-valuen
ovarian cancer4.35e-0914


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
FOSL1#8061339.7135797163731.59554825631833e-050.000370140969217304
FOSL2#2355316.93020060456170.0002060162053171620.00242353305554394
MAX#414936.452555509007120.003721913834265510.0185827019283323
MYC#460935.22228187160940.007020843755740150.0293264768630063
REST#597839.650028716128020.001112636247114590.00765447711036168



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.