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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4793_Fibroblast_Hair_Skeletal_mesodermal_Preadipocyte_neuroectodermal_Pancreatic
|full_id=C4793_Fibroblast_Hair_Skeletal_mesodermal_Preadipocyte_neuroectodermal_Pancreatic
|id=C4793
|id=C4793

Revision as of 17:56, 12 September 2012


Full id: C4793_Fibroblast_Hair_Skeletal_mesodermal_Preadipocyte_neuroectodermal_Pancreatic



Phase1 CAGE Peaks

Hg19::chr9:118358874..118358932,+p@chr9:118358874..118358932
+
Hg19::chr9:118358945..118358954,+p@chr9:118358945..118358954
+
Hg19::chr9:118358956..118358970,+p@chr9:118358956..118358970
+


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
somite2.68e-2883
paraxial mesoderm2.68e-2883
presomitic mesoderm2.68e-2883
presumptive segmental plate2.68e-2883
trunk paraxial mesoderm2.68e-2883
presumptive paraxial mesoderm2.68e-2883
dermomyotome5.30e-2670
multilaminar epithelium1.14e-2182
skeletal muscle tissue1.47e-2161
striated muscle tissue1.47e-2161
myotome1.47e-2161
muscle tissue3.57e-2063
musculature3.57e-2063
musculature of body3.57e-2063
trunk mesenchyme1.68e-14143
integument1.12e-1245
integumental system1.12e-1245
skin of body6.73e-1240
organism subdivision6.86e-12365
artery1.65e-1042
arterial blood vessel1.65e-1042
arterial system1.65e-1042
trunk4.71e-10216
systemic artery1.77e-0933
systemic arterial system1.77e-0933
surface structure2.23e-0995
splanchnic layer of lateral plate mesoderm1.75e-0884
vasculature5.09e-0879
vascular system5.09e-0879
cardiovascular system7.84e-08110
unilaminar epithelium1.84e-07138
circulatory system3.63e-07113
heart5.88e-0724
primitive heart tube5.88e-0724
primary heart field5.88e-0724
anterior lateral plate mesoderm5.88e-0724
heart tube5.88e-0724
heart primordium5.88e-0724
cardiac mesoderm5.88e-0724
cardiogenic plate5.88e-0724
heart rudiment5.88e-0724


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
CTCF#1066435.360256373075030.0064925092527670.0281649501079848



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.