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|ontology_enrichment_disease=DOID:162!9.98e-40!235;DOID:14566!1.72e-38!239;DOID:0050686!1.12e-19!137;DOID:0050687!3.07e-19!143;DOID:2531!1.11e-18!51;DOID:0060083!1.11e-18!51;DOID:305!8.74e-16!106;DOID:1240!6.10e-15!39;DOID:8692!2.03e-11!31
|ontology_enrichment_disease=DOID:162!9.98e-40!235;DOID:14566!1.72e-38!239;DOID:0050686!1.12e-19!137;DOID:0050687!3.07e-19!143;DOID:2531!1.11e-18!51;DOID:0060083!1.11e-18!51;DOID:305!8.74e-16!106;DOID:1240!6.10e-15!39;DOID:8692!2.03e-11!31
|ontology_enrichment_uberon=UBERON:0000072!2.87e-07!46;UBERON:0001737!7.21e-07!9
|ontology_enrichment_uberon=UBERON:0000072!2.87e-07!46;UBERON:0001737!7.21e-07!9
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}}
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Revision as of 17:34, 8 August 2012


Full id: C1713_Alveolar_Renal_Hodgkin_chronic_MCF7_Placental_Melanocyte



Phase1 CAGE Peaks

Hg19::chr14:104181771..104181827,-p1@XRCC3
Hg19::chr16:3030386..3030400,-p2@PKMYT1
Hg19::chr16:3030407..3030489,-p1@PKMYT1
Hg19::chr19:12917364..12917407,+p2@RNASEH2A
Hg19::chr19:14247387..14247409,-p1@ASF1B


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:0006259DNA metabolic process0.0279660708108065



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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell5.30e-24254
animal cell1.45e-20679
eukaryotic cell1.45e-20679
native cell5.00e-13722
embryonic cell3.42e-11248
migratory neural crest cell8.46e-0941
ectodermal cell3.35e-0771
neurectodermal cell5.42e-0759
squamous epithelial cell6.12e-0762
Uber Anatomy
Ontology termp-valuen
segment of respiratory tract2.87e-0746
larynx7.21e-079
Disease
Ontology termp-valuen
cancer9.98e-40235
disease of cellular proliferation1.72e-38239
organ system cancer1.12e-19137
cell type cancer3.07e-19143
hematologic cancer1.11e-1851
immune system cancer1.11e-1851
carcinoma8.74e-16106
leukemia6.10e-1539
myeloid leukemia2.03e-1131


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.