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|ontology_enrichment_disease=DOID:14566!1.82e-49!239;DOID:162!3.53e-48!235;DOID:0050687!5.05e-25!143;DOID:0050686!3.60e-22!137;DOID:305!5.73e-20!106;DOID:2531!2.37e-16!51;DOID:0060083!2.37e-16!51;DOID:1240!1.31e-13!39;DOID:8692!1.39e-10!31
|ontology_enrichment_disease=DOID:14566!1.82e-49!239;DOID:162!3.53e-48!235;DOID:0050687!5.05e-25!143;DOID:0050686!3.60e-22!137;DOID:305!5.73e-20!106;DOID:2531!2.37e-16!51;DOID:0060083!2.37e-16!51;DOID:1240!1.31e-13!39;DOID:8692!1.39e-10!31
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
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}}
}}

Revision as of 19:45, 8 August 2012


Full id: C4120_giant_peripheral_Mast_embryonic_acute_chronic_Mammary



Phase1 CAGE Peaks

Hg19::chr2:122494439..122494459,-p1@MKI67IP
Hg19::chr2:122494462..122494477,-p2@MKI67IP
Hg19::chr6:111303231..111303301,+p1@RPF2


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


GO IDGO nameFDR corrected p-value
GO:0009303rRNA transcription0.0168373955021783
GO:0000794condensed nuclear chromosome0.0200753561756741
GO:0000793condensed chromosome0.022449860669571
GO:0016072rRNA metabolic process0.0239609089838691
GO:0000228nuclear chromosome0.0256446485340869
GO:0005730nucleolus0.035617567408454



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><br>disease_data<br>


Cell Type
Ontology termp-valuen
animal cell2.21e-14679
eukaryotic cell2.21e-14679
native cell2.08e-10722
epithelial cell6.98e-08254
Disease
Ontology termp-valuen
disease of cellular proliferation1.82e-49239
cancer3.53e-48235
cell type cancer5.05e-25143
organ system cancer3.60e-22137
carcinoma5.73e-20106
hematologic cancer2.37e-1651
immune system cancer2.37e-1651
leukemia1.31e-1339
myeloid leukemia1.39e-1031


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.