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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 19:56, 8 August 2012


Full id: C4344_pleomorphic_Skeletal_Hodgkin_mesenchymal_Osteoblast_Chondrocyte_epithelioid



Phase1 CAGE Peaks

Hg19::chr3:72937182..72937270,+p1@GXYLT2
Hg19::chr3:72937278..72937291,+p3@GXYLT2
Hg19::chr3:72937303..72937320,+p2@GXYLT2


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 structure9.11e-21347
organism subdivision3.71e-20365
somite3.96e-1783
paraxial mesoderm3.96e-1783
presomitic mesoderm3.96e-1783
presumptive segmental plate3.96e-1783
trunk paraxial mesoderm3.96e-1783
presumptive paraxial mesoderm3.96e-1783
dermomyotome9.72e-1770
trunk mesenchyme1.48e-16143
skeletal muscle tissue1.58e-1661
striated muscle tissue1.58e-1661
myotome1.58e-1661
muscle tissue2.62e-1663
musculature2.62e-1663
musculature of body2.62e-1663
cell layer5.21e-15312
epithelium2.10e-14309
multilaminar epithelium5.89e-1482
trunk6.07e-14216
mesenchyme3.99e-12238
entire embryonic mesenchyme3.99e-12238
primary circulatory organ6.27e-1127
heart9.86e-1124
primitive heart tube9.86e-1124
primary heart field9.86e-1124
anterior lateral plate mesoderm9.86e-1124
heart tube9.86e-1124
heart primordium9.86e-1124
cardiac mesoderm9.86e-1124
cardiogenic plate9.86e-1124
heart rudiment9.86e-1124
anatomical cluster1.14e-10286
unilaminar epithelium2.04e-09138
multi-cellular organism5.10e-09659
compound organ1.26e-0869
epithelial tube4.13e-08118
anatomical conduit5.83e-08241
embryo3.02e-07612
tube5.19e-07194
embryonic structure6.80e-07605
developing anatomical structure6.80e-07605
splanchnic layer of lateral plate mesoderm9.27e-0784
anatomical system9.40e-07625
anatomical group9.90e-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)

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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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