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Coexpression cluster:C2725: Difference between revisions

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|full_id=C2725_clear_mesothelioma_Retinal_serous_gall_signet_bile
|full_id=C2725_clear_mesothelioma_Retinal_serous_gall_signet_bile
|id=C2725
|id=C2725
|ontology_enrichment_celltype=CL:0000077!3.94e-08!19;CL:0002586!5.35e-08!3
|ontology_enrichment_celltype=CL:0000077!2.10e-26!19;CL:0002586!1.71e-25!3;CL:0000149!2.79e-19!4;CL:0000313!1.32e-09!1;CL:0000076!4.39e-09!63;CL:0000213!6.17e-08!58;CL:0000215!6.17e-08!58
|ontology_enrichment_disease=DOID:305!8.76e-07!106
|ontology_enrichment_disease=DOID:2152!1.32e-09!1
|ontology_enrichment_uberon=UBERON:0001781!5.35e-08!3;UBERON:0001782!5.35e-08!3;UBERON:0005424!5.35e-08!3;UBERON:0000966!2.54e-07!5;UBERON:0005388!2.54e-07!5;UBERON:0001802!2.54e-07!5
|ontology_enrichment_uberon=UBERON:0001782!1.71e-25!3;UBERON:0005424!1.71e-25!3;UBERON:0001781!2.79e-19!4;UBERON:0000966!4.81e-13!6;UBERON:0005388!4.81e-13!6;UBERON:0001802!4.81e-13!6;UBERON:0004911!1.32e-09!1;UBERON:0000997!4.50e-09!1;UBERON:0005056!4.50e-09!1;UBERON:0007625!2.49e-07!11
|tf_chipseq_enrich=EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434792561188539!ESR1#2099;3:23.0764524721159:0.000133910524496857:0.00175851644259113!FOSL2#2355;3:12.6976504534213:0.00078756857297571:0.00616865713161918!FOXA1#3169;3:8.31106481203909:0.00274013818210985:0.0150390084398219!GATA3#2625;3:20.4273872679045:0.000192441557625832:0.00232056388833671!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074426990778132!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392183062346082!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000443794411664129!SRF#6722;3:10.3478836966259:0.00143989377840126:0.00924057185218442!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499519006971304
|tf_chipseq_enrich=EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434792561188539!ESR1#2099;3:23.0764524721159:0.000133910524496857:0.00175851644259113!FOSL2#2355;3:12.6976504534213:0.00078756857297571:0.00616865713161918!FOXA1#3169;3:8.31106481203909:0.00274013818210985:0.0150390084398219!GATA3#2625;3:20.4273872679045:0.000192441557625832:0.00232056388833671!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074426990778132!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392183062346082!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000443794411664129!SRF#6722;3:10.3478836966259:0.00143989377840126:0.00924057185218442!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499519006971304
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}}
}}

Revision as of 14:21, 19 October 2012


Full id: C2725_clear_mesothelioma_Retinal_serous_gall_signet_bile



Phase1 CAGE Peaks

Hg19::chr3:149191723..149191760,+p4@TM4SF4
Hg19::chr6:168250971..168250985,+p@chr6:168250971..168250985
+
Hg19::chr6:168251000..168251007,+p@chr6:168251000..168251007
+
Hg19::chr6:168251010..168251018,+p@chr6:168251010..168251018
+


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
mesothelial cell2.10e-2619
retinal pigment epithelial cell1.71e-253
visual pigment cell2.79e-194
serous secreting cell1.32e-091
squamous epithelial cell4.39e-0963
lining cell6.17e-0858
barrier cell6.17e-0858
Disease
Ontology termp-valuen
ovary epithelial cancer1.32e-091


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
EP300#203346.77394172622320.0004748459821442640.00434792561188539
ESR1#2099323.07645247211590.0001339105244968570.00175851644259113
FOSL2#2355312.69765045342130.000787568572975710.00616865713161918
FOXA1#316938.311064812039090.002740138182109850.0150390084398219
GATA3#2625320.42738726790450.0001924415576258320.00232056388833671
JUN#3725412.51282919233634.07770316866756e-050.00074426990778132
JUND#372746.994663941871030.000417684217818580.00392183062346082
NR3C1#2908414.9730233311731.98868032687801e-050.000443794411664129
SRF#6722310.34788369662590.001439893778401260.00924057185218442
TRIM28#10155313.94289378394690.0005972858184258420.00499519006971304



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.