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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:53, 8 August 2012


Full id: C3086_Mesenchymal_Chondrocyte_Olfactory_Multipotent_aorta_colon_penis



Phase1 CAGE Peaks

Hg19::chr11:117075376..117075390,+p3@uc001pqq.1
Hg19::chr11:117075397..117075445,+p2@uc001pqq.1
Hg19::chr9:35682029..35682060,-p@chr9:35682029..35682060
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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><br>

Uber Anatomy
Ontology termp-valuen
muscle tissue4.87e-1263
musculature4.87e-1263
musculature of body4.87e-1263
trunk mesenchyme1.24e-11143
skeletal muscle tissue2.06e-1161
striated muscle tissue2.06e-1161
myotome2.06e-1161
multi-cellular organism1.22e-10659
somite1.29e-1083
paraxial mesoderm1.29e-1083
presomitic mesoderm1.29e-1083
presumptive segmental plate1.29e-1083
trunk paraxial mesoderm1.29e-1083
presumptive paraxial mesoderm1.29e-1083
multilaminar epithelium1.97e-1082
dermomyotome5.42e-1070
vasculature1.20e-0979
vascular system1.20e-0979
organism subdivision1.67e-09365
trunk3.81e-09216
splanchnic layer of lateral plate mesoderm6.12e-0984
blood vessel1.42e-0860
epithelial tube open at both ends1.42e-0860
blood vasculature1.42e-0860
vascular cord1.42e-0860
anatomical system2.13e-08625
anatomical group3.08e-08626
multi-tissue structure4.65e-08347
epithelial tube6.10e-08118
artery1.25e-0742
arterial blood vessel1.25e-0742
arterial system1.25e-0742
circulatory system2.56e-07113
cardiovascular system2.60e-07110
mesenchyme4.65e-07238
entire embryonic mesenchyme4.65e-07238
unilaminar epithelium4.68e-07138
vessel7.66e-0769


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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