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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:26, 8 August 2012


Full id: C2601_meningioma_chorionic_Hepatocyte_Mesenchymal_renal_ductal_embryonic



Phase1 CAGE Peaks

Hg19::chr1:8073611..8073631,-p5@ERRFI1
Hg19::chr1:8074201..8074218,-p4@ERRFI1
Hg19::chr1:8074280..8074298,-p2@ERRFI1
Hg19::chr1:8075744..8075757,-p7@ERRFI1


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
endodermal cell3.09e-1159
non-terminally differentiated cell1.38e-08180
epithelial cell2.94e-08254
embryonic cell1.02e-07248
endo-epithelial cell1.04e-0743
Uber Anatomy
Ontology termp-valuen
organism subdivision7.02e-14365
endoderm-derived structure4.11e-13169
endoderm4.11e-13169
presumptive endoderm4.11e-13169
multi-tissue structure6.23e-13347
multi-cellular organism1.06e-12659
trunk2.22e-12216
immaterial anatomical entity4.74e-11126
embryo2.09e-10612
mesenchyme3.50e-10238
entire embryonic mesenchyme3.50e-10238
primordium7.55e-10168
embryonic structure1.03e-09605
developing anatomical structure1.03e-09605
germ layer1.29e-09604
embryonic tissue1.29e-09604
presumptive structure1.29e-09604
epiblast (generic)1.29e-09604
digestive system2.72e-09155
digestive tract2.72e-09155
primitive gut2.72e-09155
anatomical system8.17e-09625
anatomical group1.36e-08626
trunk mesenchyme1.46e-08143
mixed endoderm/mesoderm-derived structure1.63e-08130
subdivision of digestive tract2.07e-08129
endodermal part of digestive tract2.07e-08129
organ3.04e-08511
endo-epithelium6.00e-0882
exocrine gland1.08e-0731
exocrine system1.08e-0731
gland1.33e-0759
epithelial sac2.08e-0725
reproductive structure2.33e-0759
reproductive system2.33e-0759
gut epithelium2.48e-0754
sac2.61e-0726
cell layer4.67e-07312
epithelium of foregut-midgut junction6.30e-0725
anatomical boundary6.30e-0725
hepatobiliary system6.30e-0725
foregut-midgut junction6.30e-0725
septum transversum6.30e-0725
hepatic diverticulum8.38e-0722
liver primordium8.38e-0722
epithelium9.11e-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)

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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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