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Coexpression cluster:C3163: Difference between revisions

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|ontology_enrichment_disease=DOID:162!1.20e-26!235;DOID:14566!4.34e-26!239;DOID:0050687!3.17e-24!143;DOID:305!2.98e-22!106;DOID:0050686!7.45e-08!137
|ontology_enrichment_disease=DOID:162!1.20e-26!235;DOID:14566!4.34e-26!239;DOID:0050687!3.17e-24!143;DOID:305!2.98e-22!106;DOID:0050686!7.45e-08!137
|ontology_enrichment_uberon=UBERON:0001007!6.53e-08!155;UBERON:0001555!6.53e-08!155;UBERON:0007026!6.53e-08!155;UBERON:0001557!7.72e-07!19
|ontology_enrichment_uberon=UBERON:0001007!6.53e-08!155;UBERON:0001555!6.53e-08!155;UBERON:0007026!6.53e-08!155;UBERON:0001557!7.72e-07!19
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278422917734144!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323754982296598!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00435611606268221!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320535106835419!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460171086820304!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166907338939013!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00894995326623205!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242298721476566!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000253103963679081!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443083390212268!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156185164509264!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185809253793908!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172349714398126!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136079366094676!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00879624020853129!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245501962070606!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641526026726772!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00241975639828952
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}}
}}

Revision as of 14:03, 5 September 2012


Full id: C3163_lymphoma_acute_epidermoid_small_signet_gall_Burkitt



Phase1 CAGE Peaks

Hg19::chr11:58874671..58874686,+p2@FAM111B
Hg19::chr11:58874689..58874700,+p3@FAM111B
Hg19::chr11:58874701..58874717,+p1@FAM111B


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 cell1.87e-13254
lymphocyte of B lineage1.10e-1024
pro-B cell1.10e-1024
neural cell1.53e-0825
Uber Anatomy
Ontology termp-valuen
digestive system6.53e-08155
digestive tract6.53e-08155
primitive gut6.53e-08155
upper respiratory tract7.72e-0719
Disease
Ontology termp-valuen
cancer1.20e-26235
disease of cellular proliferation4.34e-26239
cell type cancer3.17e-24143
carcinoma2.98e-22106
organ system cancer7.45e-08137


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
CTCF#1066435.360256373075030.0064925092527670.0278422917734144
E2F1#186934.907389214879320.008460985347239390.0323754982296598
E2F4#1874312.66806031528440.0004917987006298980.00435611606268221
E2F6#187635.017155731697390.00791769806886330.0320535106835419
ELF1#199734.258097958807540.01295179875054610.0460171086820304
EP300#203336.77394172622320.003216880500103790.0166907338939013
FOS#235338.99795530889440.001372499272417130.00894995326623205
FOSL2#2355316.93020060456170.0002060162053171620.00242298721476566
IRF3#3661346.98195221148969.63568551583244e-060.000253103963679081
JUN#3725312.51282919233630.0005103313992726250.00443083390212268
JUND#372736.994663941871030.002921845042734990.0156185164509264
MAX#414936.452555509007120.003721913834265510.0185809253793908
PAX5#507936.669565531177830.003370290999677260.0172349714398126
PBX3#5090321.91451268674419.49854535978121e-050.00136079366094676
POU2F2#545239.106124057742520.001324165192682130.00879624020853129
SP1#666735.69838137814090.005403962701712170.0245501962070606
STAT3#6774310.51946499715420.0008589184530415310.00641526026726772
ZEB1#6935316.88843201754390.0002075486917327580.00241975639828952



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.