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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1751_Mesenchymal_Fibroblast_tenocyte_Smooth_Synoviocyte_Hair_Preadipocyte
|full_id=C1751_Mesenchymal_Fibroblast_tenocyte_Smooth_Synoviocyte_Hair_Preadipocyte
|id=C1751
|id=C1751

Revision as of 14:21, 12 September 2012


Full id: C1751_Mesenchymal_Fibroblast_tenocyte_Smooth_Synoviocyte_Hair_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr15:74466034..74466097,+p2@ISLR
Hg19::chr15:74466124..74466168,+p3@ISLR
Hg19::chr15:74466169..74466212,+p4@ISLR
Hg19::chr15:74466233..74466257,+p5@ISLR
Hg19::chr15:74466268..74466273,+p10@ISLR


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
organism subdivision1.93e-17365
adult organism5.03e-16115
dermomyotome1.20e-1570
somite1.93e-1583
paraxial mesoderm1.93e-1583
presomitic mesoderm1.93e-1583
presumptive segmental plate1.93e-1583
trunk paraxial mesoderm1.93e-1583
presumptive paraxial mesoderm1.93e-1583
muscle tissue3.14e-1563
musculature3.14e-1563
musculature of body3.14e-1563
skeletal muscle tissue1.45e-1461
striated muscle tissue1.45e-1461
myotome1.45e-1461
multilaminar epithelium7.21e-1282
multi-tissue structure2.13e-11347
multi-cellular organism6.60e-10659
anatomical cluster2.47e-09286
trunk mesenchyme9.55e-09143
primary circulatory organ1.44e-0827
splanchnic layer of lateral plate mesoderm2.51e-0884
tissue2.90e-08787
heart4.13e-0824
primitive heart tube4.13e-0824
primary heart field4.13e-0824
anterior lateral plate mesoderm4.13e-0824
heart tube4.13e-0824
heart primordium4.13e-0824
cardiac mesoderm4.13e-0824
cardiogenic plate4.13e-0824
heart rudiment4.13e-0824
cell layer5.72e-08312
adipose tissue7.20e-0814
regional part of brain8.26e-0859
epithelium2.31e-07309
anatomical group3.03e-07626
anatomical system3.93e-07625
anatomical conduit4.35e-07241
systemic artery5.44e-0733
systemic arterial system5.44e-0733
neural tube6.23e-0757
neural rod6.23e-0757
future spinal cord6.23e-0757
neural keel6.23e-0757


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
EP300#203356.77394172622327.00901578206049e-050.00110793794348814



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.