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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3343_heart_aorta_cervix_prostate_penis_rectum_smooth
|full_id=C3343_heart_aorta_cervix_prostate_penis_rectum_smooth
|gostat_on_coexpression_clusters=GO:0005578!proteinaceous extracellular matrix!0.0337609163535741!1634;8425$GO:0030162!regulation of proteolysis!0.0337609163535741!8425$GO:0004675!transmembrane receptor protein serine/threonine kinase activity!0.0337609163535741!8425$GO:0005024!transforming growth factor beta receptor activity!0.0337609163535741!8425$GO:0044421!extracellular region part!0.0359035381252379!1634;8425
|gostat_on_coexpression_clusters=GO:0005578!proteinaceous extracellular matrix!0.0337609163535741!1634;8425$GO:0030162!regulation of proteolysis!0.0337609163535741!8425$GO:0004675!transmembrane receptor protein serine/threonine kinase activity!0.0337609163535741!8425$GO:0005024!transforming growth factor beta receptor activity!0.0337609163535741!8425$GO:0044421!extracellular region part!0.0359035381252379!1634;8425

Revision as of 16:15, 12 September 2012


Full id: C3343_heart_aorta_cervix_prostate_penis_rectum_smooth



Phase1 CAGE Peaks

Hg19::chr12:91576750..91576805,-p7@DCN
Hg19::chr16:49698178..49698209,-p1@ZNF423
Hg19::chr19:41107249..41107295,+p1@LTBP4


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

GO IDGO nameFDR corrected p-value
GO:0005578proteinaceous extracellular matrix0.0337609163535741
GO:0030162regulation of proteolysis0.0337609163535741
GO:0004675transmembrane receptor protein serine/threonine kinase activity0.0337609163535741
GO:0005024transforming growth factor beta receptor activity0.0337609163535741
GO:0044421extracellular region part0.0359035381252379



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism6.44e-28115
anatomical cluster1.91e-11286
multi-tissue structure2.22e-11347
organism subdivision2.40e-09365
anterior region of body3.87e-09129
craniocervical region3.87e-09129
multi-cellular organism9.64e-09659
endoderm-derived structure1.05e-08169
endoderm1.05e-08169
presumptive endoderm1.05e-08169
anatomical conduit1.39e-08241
epithelium1.79e-08309
ectoderm1.93e-08173
presumptive ectoderm1.93e-08173
head2.36e-08123
cell layer2.82e-08312
ectoderm-derived structure4.81e-08169
digestive system1.16e-07155
digestive tract1.16e-07155
primitive gut1.16e-07155
organ1.93e-07511
surface structure2.07e-0795
orifice4.30e-0735
neurectoderm5.38e-0790
anatomical system5.77e-07625
anatomical group9.34e-07626


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

No analysis results for this cluster

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.

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