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Coexpression cluster:C2379: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106434457043511!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.60141368515537e-05
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106434457043511!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.60141368515537e-05
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}}
}}

Revision as of 15:27, 26 November 2012


Full id: C2379_smallcell_maxillary_malignant_kidney_pancreatic_signet_bronchioalveolar



Phase1 CAGE Peaks

Hg19::chr16:57653596..57653610,+p10@GPR56
Hg19::chr16:57653625..57653669,+p3@GPR56
Hg19::chr16:57653946..57653968,+p4@GPR56
Hg19::chr16:57653997..57654022,+p7@GPR56


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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.26e-35160
endoderm9.26e-35160
presumptive endoderm9.26e-35160
digestive system2.38e-27145
digestive tract2.38e-27145
primitive gut2.38e-27145
subdivision of digestive tract1.99e-25118
respiratory system1.03e-2174
foregut1.70e-1987
respiratory tract1.72e-1654
trunk region element3.94e-14101
renal system4.81e-1448
endo-epithelium5.44e-1482
immaterial anatomical entity9.70e-14117
urinary system structure1.39e-1347
respiratory primordium2.37e-1338
endoderm of foregut2.37e-1338
anatomical space5.17e-1395
segment of respiratory tract3.48e-1247
organ1.44e-11503
subdivision of trunk7.10e-11112
epithelial bud9.57e-1137
orifice6.45e-1036
thoracic cavity element8.83e-1034
thoracic cavity8.83e-1034
thoracic segment organ2.69e-0935
organism subdivision2.76e-09264
internal genitalia7.08e-0925
reproductive structure1.15e-0859
reproductive system1.15e-0859
epithelial fold1.17e-0847
oral opening1.86e-0822
reproductive organ4.79e-0848
organ part5.13e-08218
lung6.84e-0822
respiratory tube6.84e-0822
respiration organ6.84e-0822
pair of lungs6.84e-0822
lung primordium6.84e-0822
lung bud6.84e-0822
nephron tubule epithelium8.00e-0810
thoracic segment of trunk1.54e-0752
respiratory system epithelium1.74e-0728
primordium1.76e-07160
kidney3.10e-0726
kidney mesenchyme3.10e-0726
upper urinary tract3.10e-0726
kidney rudiment3.10e-0726
kidney field3.10e-0726
multi-cellular organism3.59e-07656
extraembryonic membrane5.01e-0714
membranous layer5.01e-0714
gland5.12e-0759
cavitated compound organ6.24e-0731
female organism6.26e-0741
embryo6.47e-07592
Disease
Ontology termp-valuen
carcinoma2.04e-27106
cell type cancer6.63e-19143
squamous cell carcinoma8.12e-1114
adenocarcinoma4.41e-0925
cancer8.40e-07235


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
E2F1#186944.907389214879320.001724022357361790.0106434457043511
ESR1#2099430.76860329615451.11467714392546e-064.60141368515537e-05



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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