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Coexpression cluster:C3254: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000473!2.68e-26!8;UBERON:0003135!4.12e-19!11;UBERON:0003101!2.68e-13!22;UBERON:0000079!2.68e-13!22;UBERON:0002110!5.58e-12!3;UBERON:0006242!5.58e-12!3;UBERON:0001764!3.74e-10!1;UBERON:0001825!3.74e-10!1;UBERON:0004458!5.78e-10!49;UBERON:0000991!6.04e-10!21;UBERON:0009196!6.04e-10!21;UBERON:0009117!6.04e-10!21;UBERON:0005564!6.04e-10!21;UBERON:0004176!1.74e-09!22;UBERON:0002323!3.48e-08!46;UBERON:0002553!8.34e-08!61;UBERON:0003886!7.40e-07!54
|ontology_enrichment_uberon=UBERON:0000473!2.68e-26!8;UBERON:0003135!4.12e-19!11;UBERON:0003101!2.68e-13!22;UBERON:0000079!2.68e-13!22;UBERON:0002110!5.58e-12!3;UBERON:0006242!5.58e-12!3;UBERON:0001764!3.74e-10!1;UBERON:0001825!3.74e-10!1;UBERON:0004458!5.78e-10!49;UBERON:0000991!6.04e-10!21;UBERON:0009196!6.04e-10!21;UBERON:0009117!6.04e-10!21;UBERON:0005564!6.04e-10!21;UBERON:0004176!1.74e-09!22;UBERON:0002323!3.48e-08!46;UBERON:0002553!8.34e-08!61;UBERON:0003886!7.40e-07!54
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}}
}}

Revision as of 16:01, 26 November 2012


Full id: C3254_maxillary_adenocarcinoma_testicular_testis_synovial_small_peripheral



Phase1 CAGE Peaks

Hg19::chr12:130822417..130822439,+p2@PIWIL1
Hg19::chr12:130822445..130822458,+p3@PIWIL1
Hg19::chr12:130822467..130822489,+p4@PIWIL1


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 cell of stomach3.37e-123
germ line cell2.01e-117
germ cell2.01e-117
Uber Anatomy
Ontology termp-valuen
testis2.68e-268
male reproductive organ4.12e-1911
male organism2.68e-1322
male reproductive system2.68e-1322
gallbladder5.58e-123
gall bladder primordium5.58e-123
maxillary sinus3.74e-101
paranasal sinus3.74e-101
body cavity or lining5.78e-1049
gonad6.04e-1021
indifferent external genitalia6.04e-1021
indifferent gonad6.04e-1021
gonad primordium6.04e-1021
external genitalia1.74e-0922
body cavity3.48e-0846
anatomical cavity8.34e-0861
body cavity precursor7.40e-0754
Disease
Ontology termp-valuen
paranasal sinus cancer3.74e-101
maxillary sinus cancer3.74e-101


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.