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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3076_Astrocyte_Preadipocyte_mesenchymal_Fibroblast_Neural_Adipocyte_Neurons
|full_id=C3076_Astrocyte_Preadipocyte_mesenchymal_Fibroblast_Neural_Adipocyte_Neurons
|id=C3076
|id=C3076

Revision as of 15:56, 12 September 2012


Full id: C3076_Astrocyte_Preadipocyte_mesenchymal_Fibroblast_Neural_Adipocyte_Neurons



Phase1 CAGE Peaks

Hg19::chr11:103673814..103673817,-p@chr11:103673814..103673817
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Hg19::chr11:103673856..103673877,-p@chr11:103673856..103673877
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Hg19::chr11:103673881..103673894,-p@chr11:103673881..103673894
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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
primary circulatory organ7.66e-1927
heart1.10e-1724
primitive heart tube1.10e-1724
primary heart field1.10e-1724
anterior lateral plate mesoderm1.10e-1724
heart tube1.10e-1724
heart primordium1.10e-1724
cardiac mesoderm1.10e-1724
cardiogenic plate1.10e-1724
heart rudiment1.10e-1724
splanchnic layer of lateral plate mesoderm1.64e-1584
compound organ2.52e-1069
circulatory system1.49e-09113
epithelial tube2.16e-09118
right ovary5.12e-095
cardiovascular system1.09e-08110
artery1.40e-0842
arterial blood vessel1.40e-0842
arterial system1.40e-0842
artery wall5.16e-084
tunica adventitia of artery5.16e-084
adventitia5.16e-084
tunica adventitia of blood vessel5.16e-084
aorta tunica adventitia5.16e-084
aorta wall5.16e-084
systemic artery6.16e-0833
systemic arterial system6.16e-0833
omentum9.72e-086
peritoneum9.72e-086
abdominal cavity9.72e-086
visceral peritoneum9.72e-086
female gonad1.60e-0713
blood vessel5.41e-0760
epithelial tube open at both ends5.41e-0760
blood vasculature5.41e-0760
vascular cord5.41e-0760
Disease
Ontology termp-valuen
ovarian cancer1.74e-1014


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
FOS#235338.99795530889440.001372499272417130.00894771857128418



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.