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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:44, 8 August 2012


Full id: C2940_renal_hairy_Mesenchymal_leiomyoblastoma_small_Hep2_Wilms



Phase1 CAGE Peaks

Hg19::chr9:139744155..139744222,+p2@PHPT1
Hg19::chr9:139744237..139744257,+p8@PHPT1
Hg19::chr9:139744264..139744275,+p10@PHPT1
Hg19::chr9:139744298..139744325,+p5@PHPT1


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
multi-tissue structure4.60e-25347
organism subdivision1.22e-20365
mesenchyme6.26e-18238
entire embryonic mesenchyme6.26e-18238
trunk7.75e-14216
trunk mesenchyme1.91e-13143
anatomical cluster1.86e-12286
somite4.83e-1283
paraxial mesoderm4.83e-1283
presomitic mesoderm4.83e-1283
presumptive segmental plate4.83e-1283
trunk paraxial mesoderm4.83e-1283
presumptive paraxial mesoderm4.83e-1283
multi-cellular organism5.19e-12659
epithelium1.61e-11309
cell layer4.71e-11312
multilaminar epithelium7.19e-1182
dermomyotome1.79e-0970
anatomical system2.52e-09625
anatomical group2.72e-09626
skeletal muscle tissue4.65e-0961
striated muscle tissue4.65e-0961
myotome4.65e-0961
endoderm-derived structure6.93e-09169
endoderm6.93e-09169
presumptive endoderm6.93e-09169
muscle tissue7.52e-0963
musculature7.52e-0963
musculature of body7.52e-0963
primordium3.28e-08168
anatomical conduit5.25e-08241
larynx1.42e-079
surface structure1.81e-0795
embryo2.51e-07612
germ layer3.60e-07604
embryonic tissue3.60e-07604
presumptive structure3.60e-07604
epiblast (generic)3.60e-07604
embryonic structure3.68e-07605
developing anatomical structure3.68e-07605
digestive system5.86e-07155
digestive tract5.86e-07155
primitive gut5.86e-07155


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)

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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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