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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1107_Myoblast_mesenchymal_skeletal_diaphragm_tongue_Prostate_penis
|full_id=C1107_Myoblast_mesenchymal_skeletal_diaphragm_tongue_Prostate_penis
|id=C1107
|id=C1107

Revision as of 13:34, 12 September 2012


Full id: C1107_Myoblast_mesenchymal_skeletal_diaphragm_tongue_Prostate_penis



Phase1 CAGE Peaks

Hg19::chr10:117419477..117419497,+p@chr10:117419477..117419497
+
Hg19::chr11:19619742..19619759,+p@chr11:19619742..19619759
+
Hg19::chr4:177190139..177190150,-p6@ASB5
Hg19::chr4:177190304..177190315,-p3@ASB5
Hg19::chr4:177190364..177190379,-p1@ASB5
Hg19::chr9:113431029..113431050,+p2@MUSK
Hg19::chr9:113431060..113431077,+p1@MUSK


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>

Cell Type
Ontology termp-valuen
cell of skeletal muscle6.48e-109
Uber Anatomy
Ontology termp-valuen
adult organism3.76e-28115
multi-tissue structure5.78e-14347
anterior region of body2.20e-13129
craniocervical region2.20e-13129
head9.82e-13123
organism subdivision1.35e-12365
multi-cellular organism1.16e-09659
ectoderm-derived structure1.88e-09169
somite2.90e-0983
paraxial mesoderm2.90e-0983
presomitic mesoderm2.90e-0983
presumptive segmental plate2.90e-0983
trunk paraxial mesoderm2.90e-0983
presumptive paraxial mesoderm2.90e-0983
ectoderm3.19e-09173
presumptive ectoderm3.19e-09173
anatomical system3.53e-09625
anatomical group4.45e-09626
central nervous system5.46e-0982
neural plate9.57e-0986
presumptive neural plate9.57e-0986
organ1.40e-08511
neurectoderm2.38e-0890
brain3.16e-0869
future brain3.16e-0869
regional part of nervous system3.75e-0894
nervous system3.75e-0894
neural tube7.57e-0857
neural rod7.57e-0857
future spinal cord7.57e-0857
neural keel7.57e-0857
embryo1.20e-07612
muscle tissue1.41e-0763
musculature1.41e-0763
musculature of body1.41e-0763
germ layer1.74e-07604
embryonic tissue1.74e-07604
presumptive structure1.74e-07604
epiblast (generic)1.74e-07604
organ part1.92e-07219
regional part of brain2.11e-0759
embryonic structure2.14e-07605
developing anatomical structure2.14e-07605
cell layer3.66e-07312
mixed ectoderm/mesoderm/endoderm-derived structure6.06e-0718
epithelium7.36e-07309


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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