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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1786_diaphragm_Olfactory_Cardiac_hepatic_tridermal_umbilical_sacrococcigeal
|full_id=C1786_diaphragm_Olfactory_Cardiac_hepatic_tridermal_umbilical_sacrococcigeal
|id=C1786
|id=C1786

Revision as of 14:24, 12 September 2012


Full id: C1786_diaphragm_Olfactory_Cardiac_hepatic_tridermal_umbilical_sacrococcigeal



Phase1 CAGE Peaks

Hg19::chr17:48262965..48262976,-p38@COL1A1
Hg19::chr7:94058505..94058512,+p@chr7:94058505..94058512
+
Hg19::chr7:94059695..94059708,+p@chr7:94059695..94059708
+
Hg19::chr7:94059753..94059773,+p@chr7:94059753..94059773
+
Hg19::chr7:94060167..94060180,+p@chr7:94060167..94060180
+


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
skeletal muscle tissue3.25e-1961
striated muscle tissue3.25e-1961
myotome3.25e-1961
somite4.28e-1983
paraxial mesoderm4.28e-1983
presomitic mesoderm4.28e-1983
presumptive segmental plate4.28e-1983
trunk paraxial mesoderm4.28e-1983
presumptive paraxial mesoderm4.28e-1983
muscle tissue5.55e-1963
musculature5.55e-1963
musculature of body5.55e-1963
dermomyotome5.98e-1870
multilaminar epithelium1.67e-1382
trunk mesenchyme6.79e-12143
splanchnic layer of lateral plate mesoderm2.64e-0984
heart9.32e-0924
primitive heart tube9.32e-0924
primary heart field9.32e-0924
anterior lateral plate mesoderm9.32e-0924
heart tube9.32e-0924
heart primordium9.32e-0924
cardiac mesoderm9.32e-0924
cardiogenic plate9.32e-0924
heart rudiment9.32e-0924
trunk3.08e-08216
primary circulatory organ2.22e-0727
organism subdivision2.91e-07365


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.