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Coexpression cluster:C1497: Difference between revisions

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|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380540854536047
|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380540854536047
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}}
}}

Revision as of 14:56, 26 November 2012


Full id: C1497_amniotic_Mallassezderived_Prostate_Urothelial_papillotubular_Gingival_Amniotic



Phase1 CAGE Peaks

Hg19::chr2:161056746..161056753,-p6@ITGB6
Hg19::chr2:161056762..161056799,-p1@ITGB6
Hg19::chr2:161056802..161056815,-p2@ITGB6
Hg19::chr2:161056820..161056825,-p4@ITGB6
Hg19::chr3:111314186..111314204,-p1@ZBED2
Hg19::chr3:111314230..111314241,-p2@ZBED2


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:0005178integrin binding0.0397168392103577
GO:0008305integrin complex0.0397168392103577
GO:0007229integrin-mediated signaling pathway0.0397168392103577
GO:0007160cell-matrix adhesion0.0397168392103577
GO:0032403protein complex binding0.0397168392103577
GO:0031589cell-substrate adhesion0.0397168392103577
GO:0043235receptor complex0.0397168392103577



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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.56e-28160
endoderm1.56e-28160
presumptive endoderm1.56e-28160
digestive system1.16e-19145
digestive tract1.16e-19145
primitive gut1.16e-19145
respiratory system4.06e-1674
urinary system structure7.75e-1647
subdivision of digestive tract2.52e-15118
renal system2.54e-1548
extraembryonic membrane7.65e-1514
membranous layer7.65e-1514
endo-epithelium8.67e-1482
respiratory tract1.70e-1254
thoracic cavity element5.47e-1234
thoracic cavity5.47e-1234
epithelial bud1.02e-1137
thoracic segment organ1.81e-1135
chorion8.65e-117
organ part2.38e-10218
epithelial fold5.51e-1047
trunk region element5.61e-10101
organ9.13e-10503
anatomical space1.05e-0995
orifice2.03e-0936
mucosa6.10e-0920
nephron tubule epithelium6.62e-0910
lung1.13e-0822
respiratory tube1.13e-0822
respiration organ1.13e-0822
pair of lungs1.13e-0822
lung primordium1.13e-0822
lung bud1.13e-0822
respiratory system epithelium2.36e-0828
organism subdivision2.41e-08264
extraembryonic structure2.60e-0824
foregut2.64e-0887
urothelium3.77e-085
immaterial anatomical entity7.27e-08117
respiratory primordium8.86e-0838
endoderm of foregut8.86e-0838
tracheobronchial tree1.22e-0715
lower respiratory tract1.22e-0715
oral opening1.74e-0722
segment of respiratory tract2.14e-0747
reproductive structure2.27e-0759
reproductive system2.27e-0759
embryo2.76e-07592
internal genitalia2.96e-0725
thoracic segment of trunk2.97e-0752
subdivision of trunk3.28e-07112
organ component layer3.51e-0766
excretory tube3.77e-0716
kidney epithelium3.77e-0716
intestine4.23e-0717
multi-cellular organism6.03e-07656
developing anatomical structure6.99e-07581
placenta7.27e-074
allantois7.27e-074
Disease
Ontology termp-valuen
squamous cell carcinoma1.46e-1314
carcinoma2.35e-09106
adenocarcinoma9.05e-0825


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
POLR2A#543062.147453176558070.01019570676818780.0380540854536047



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.

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