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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0000468!5.72e-20!659;UBERON:0007023!1.30e-18!115;UBERON:0000467!2.04e-16!625;UBERON:0002371!4.58e-16!80;UBERON:0000922!5.02e-16!612;UBERON:0000480!5.22e-16!626;UBERON:0002050!8.15e-16!605;UBERON:0005423!8.15e-16!605;UBERON:0002390!1.15e-15!102;UBERON:0003061!1.15e-15!102;UBERON:0000923!1.26e-15!604;UBERON:0005291!1.26e-15!604;UBERON:0006598!1.26e-15!604;UBERON:0002532!1.26e-15!604;UBERON:0001474!1.38e-15!86;UBERON:0002405!2.61e-15!115;UBERON:0002193!1.54e-14!112;UBERON:0004765!5.21e-14!101;UBERON:0001434!5.21e-14!101;UBERON:0000062!5.68e-14!511;UBERON:0000926!4.33e-09!448;UBERON:0004120!4.33e-09!448;UBERON:0006603!4.33e-09!448;UBERON:0002204!2.21e-08!167;UBERON:0003081!4.47e-08!216;UBERON:0004119!1.99e-07!169;UBERON:0000925!1.99e-07!169;UBERON:0006595!1.99e-07!169;UBERON:0001007!7.48e-07!155;UBERON:0001555!7.48e-07!155;UBERON:0007026!7.48e-07!155
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}}
}}

Revision as of 20:20, 8 August 2012


Full id: C4808_Hepatocyte_keratoacanthoma_salivary_breast_liver_oral_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr9:137218281..137218340,+p1@RXRA
Hg19::chr9:137218341..137218361,+p2@RXRA
Hg19::chr9:137218362..137218385,+p4@RXRA


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-cellular organism5.72e-20659
adult organism1.30e-18115
anatomical system2.04e-16625
bone marrow4.58e-1680
embryo5.02e-16612
anatomical group5.22e-16626
embryonic structure8.15e-16605
developing anatomical structure8.15e-16605
hematopoietic system1.15e-15102
blood island1.15e-15102
germ layer1.26e-15604
embryonic tissue1.26e-15604
presumptive structure1.26e-15604
epiblast (generic)1.26e-15604
bone element1.38e-1586
immune system2.61e-15115
hemolymphoid system1.54e-14112
skeletal element5.21e-14101
skeletal system5.21e-14101
organ5.68e-14511
mesoderm4.33e-09448
mesoderm-derived structure4.33e-09448
presumptive mesoderm4.33e-09448
musculoskeletal system2.21e-08167
lateral plate mesoderm4.47e-08216
endoderm-derived structure1.99e-07169
endoderm1.99e-07169
presumptive endoderm1.99e-07169
digestive system7.48e-07155
digestive tract7.48e-07155
primitive gut7.48e-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.