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Coexpression cluster:C2562: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106541521290241!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434487817847948!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.610525395423e-05!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074362011739562!JUNB#3726;4:30.6106326598211:1.13787152942193e-06:4.66032018279597e-05!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391901195083592!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157139068550556!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241746320597381!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.00043817813892143!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123192714552934!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000326653726613121!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114593343073223
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106541521290241!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434487817847948!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.610525395423e-05!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.00074362011739562!JUNB#3726;4:30.6106326598211:1.13787152942193e-06:4.66032018279597e-05!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391901195083592!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157139068550556!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241746320597381!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.00043817813892143!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123192714552934!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000326653726613121!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114593343073223
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}}
}}

Revision as of 15:35, 26 November 2012


Full id: C2562_Urothelial_Gingival_Keratinocyte_Mammary_Bronchial_Small_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr1:209826369..209826380,-p@chr1:209826369..209826380
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Hg19::chr1:209826396..209826431,-p@chr1:209826396..209826431
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Hg19::chr1:209826442..209826464,-p@chr1:209826442..209826464
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Hg19::chr1:209826486..209826491,-p@chr1:209826486..209826491
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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 structure4.43e-23160
endoderm4.43e-23160
presumptive endoderm4.43e-23160
digestive system1.04e-15145
digestive tract1.04e-15145
primitive gut1.04e-15145
subdivision of digestive tract1.41e-13118
urinary system structure1.68e-1347
renal system5.24e-1348
respiratory system1.64e-1274
respiratory tract1.96e-1254
respiratory primordium2.98e-1238
endoderm of foregut2.98e-1238
endo-epithelium2.09e-1082
extraembryonic membrane5.68e-1014
membranous layer5.68e-1014
epithelial bud9.10e-1037
segment of respiratory tract2.18e-0847
epithelial fold4.63e-0847
organ4.75e-08503
thoracic cavity element6.41e-0834
thoracic cavity6.41e-0834
foregut7.16e-0887
thoracic segment organ1.60e-0735
chorion2.02e-077
trunk region element3.00e-07101
tracheobronchial tree3.04e-0715
lower respiratory tract3.04e-0715
transitional epithelium4.10e-076
urothelium5.85e-075
organ part7.54e-07218
mucosa8.43e-0720
nephron tubule epithelium9.47e-0710
Disease
Ontology termp-valuen
carcinoma1.53e-20106
cell type cancer5.28e-15143
squamous cell carcinoma5.23e-1014
adenocarcinoma7.50e-0925


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#186944.907389214879320.001724022357361790.0106541521290241
EP300#203346.77394172622320.0004748459821442640.00434487817847948
ESR1#2099430.76860329615451.11467714392546e-064.610525395423e-05
JUN#3725412.51282919233634.07770316866756e-050.00074362011739562
JUNB#3726430.61063265982111.13787152942193e-064.66032018279597e-05
JUND#372746.994663941871030.000417684217818580.00391901195083592
REST#597849.650028716128020.0001152825614219170.00157139068550556
SMARCB1#6598418.25271578115749.00423392720929e-060.000241746320597381
SMC3#9126415.04493284493281.95092670935632e-050.00043817813892143
STAT3#6774410.51946499715428.16377768286615e-050.00123192714552934
TFAP2A#7020416.5186343730451.34240829060362e-050.000326653726613121
TFAP2C#7022410.80922860986027.32289634782688e-050.00114593343073223



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.