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|ontology_enrichment_disease=DOID:120!2.37e-09!27;DOID:193!9.11e-09!29;DOID:2394!3.75e-07!14
|ontology_enrichment_disease=DOID:120!2.37e-09!27;DOID:193!9.11e-09!29;DOID:2394!3.75e-07!14
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|ontology_enrichment_uberon=UBERON:0000475!7.23e-12!365;UBERON:0002100!4.82e-10!216;UBERON:0003914!4.47e-09!118;UBERON:0003886!4.48e-09!63;UBERON:0000481!6.00e-09!347;UBERON:0000119!1.03e-08!312;UBERON:0000483!2.22e-08!309;UBERON:0004111!3.46e-08!241;UBERON:0000464!4.82e-08!104;UBERON:0000025!2.08e-07!194;UBERON:0000466!2.31e-07!126;UBERON:0003100!4.45e-07!41;UBERON:0001008!5.95e-07!45;UBERON:0003104!6.17e-07!238;UBERON:0009142!6.17e-07!238;UBERON:0002553!6.78e-07!70;UBERON:0000477!8.54e-07!286;UBERON:0006554!9.24e-07!44
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}}
}}

Revision as of 20:57, 8 August 2012


Full id: C893_osteoclastoma_Urothelial_tubular_nonsmall_Mesenchymal_Renal_hepatic



Phase1 CAGE Peaks

Hg19::chr12:47473475..47473484,-p9@AMIGO2
Hg19::chr12:47473520..47473544,-p3@AMIGO2
Hg19::chr12:47473557..47473568,-p8@AMIGO2
Hg19::chr12:47473642..47473653,-p7@AMIGO2
Hg19::chr12:47473707..47473757,-p1@AMIGO2
Hg19::chr12:47473898..47473903,-p11@AMIGO2
Hg19::chr12:47473904..47473917,-p6@AMIGO2
Hg19::chr12:47473920..47473939,-p5@AMIGO2
Hg19::chr12:47474192..47474251,-p4@AMIGO2


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell1.20e-10254
endo-epithelial cell4.73e-0843
embryonic cell1.19e-07248
vascular associated smooth muscle cell7.10e-0732
Uber Anatomy
Ontology termp-valuen
organism subdivision7.23e-12365
trunk4.82e-10216
epithelial tube4.47e-09118
body cavity precursor4.48e-0963
multi-tissue structure6.00e-09347
cell layer1.03e-08312
epithelium2.22e-08309
anatomical conduit3.46e-08241
anatomical space4.82e-08104
tube2.08e-07194
immaterial anatomical entity2.31e-07126
female organism4.45e-0741
renal system5.95e-0745
mesenchyme6.17e-07238
entire embryonic mesenchyme6.17e-07238
anatomical cavity6.78e-0770
anatomical cluster8.54e-07286
urinary system structure9.24e-0744
Disease
Ontology termp-valuen
female reproductive organ cancer2.37e-0927
reproductive organ cancer9.11e-0929
ovarian cancer3.75e-0714


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.