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Difference between revisions of "Coexpression cluster:C4761"

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|ontology_enrichment_disease=DOID:14566!1.17e-41!239;DOID:162!1.74e-41!235;DOID:0050687!1.82e-25!143;DOID:305!1.16e-19!106;DOID:0050686!1.91e-19!137;DOID:7!2.56e-08!39
 
|ontology_enrichment_disease=DOID:14566!1.17e-41!239;DOID:162!1.74e-41!235;DOID:0050687!1.82e-25!143;DOID:305!1.16e-19!106;DOID:0050686!1.91e-19!137;DOID:7!2.56e-08!39
 
|ontology_enrichment_uberon=UBERON:0004458!5.89e-08!49;UBERON:0002323!1.38e-07!46
 
|ontology_enrichment_uberon=UBERON:0004458!5.89e-08!49;UBERON:0002323!1.38e-07!46
 +
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191323858407629!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115858688394741!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327960528756062!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00439224940098221!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324586461223902!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00919474352213078!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322713751612852!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0465203738249573!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168590818220765!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00765777928485838!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154898133260248!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00393822948583633!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109317461729864!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128802519551111!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187494192039772!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195468288041549!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00723788776009257!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296250616543067!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270945787565502!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000606626714118834!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310464049945816!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173744914218517!REST#5978;3:9.65002871612802:0.00111263624711459:0.00771751457876075!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.0016607700663996!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278458257392176!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00240383690591062!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0248037470600385!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376690417547419!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054604244764961!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00632240684491891!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331410102414523!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0141045108304004!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00390605990546314
 
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}}
 
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Revision as of 04:53, 5 September 2012


Full id: C4761_testicular_Wilms_mucinous_lung_large_H9_mesothelioma



Phase1 CAGE Peaks

Hg19::chr8:54934889..54934901,-p5@TCEA1
Hg19::chr8:54934917..54934938,-p3@TCEA1
Hg19::chr8:54934978..54935000,-p2@TCEA1


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
animal cell8.77e-23679
eukaryotic cell8.77e-23679
native cell1.04e-13722
epithelial cell3.56e-10254
Uber Anatomy
Ontology termp-valuen
body cavity or lining5.89e-0849
body cavity1.38e-0746
Disease
Ontology termp-valuen
disease of cellular proliferation1.17e-41239
cancer1.74e-41235
cell type cancer1.82e-25143
carcinoma1.16e-19106
organ system cancer1.91e-19137
disease of anatomical entity2.56e-0839


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
CCNT2#90536.336201576962630.003930750035764890.0191323858407629
CEBPB#105137.971147625824820.001974187055288560.0115858688394741
E2F1#186934.907389214879320.008460985347239390.0327960528756062
E2F4#1874312.66806031528440.0004917987006298980.00439224940098221
E2F6#187635.017155731697390.00791769806886330.0324586461223902
EBF1#187938.9064668465690.00141523283560980.00919474352213078
EGR1#195834.988179094810140.008056488137383440.0322713751612852
ELF1#199734.258097958807540.01295179875054610.0465203738249573
EP300#203336.77394172622320.003216880500103790.0168590818220765
ETS1#211339.728760922202340.001085840092584840.00765777928485838
GABPB1#255337.067683836182170.002832212825417420.0154898133260248
HDAC2#3066313.41562023662630.0004140761399857210.00393822948583633
HMGN3#932438.178547723350590.001827766942164210.0109317461729864
IRF1#365937.63716375356390.002244692747297240.0128802519551111
MAX#414936.452555509007120.003721913834265510.0187494192039772
MEF2A#4205318.74323090964410.0001518243905622470.00195468288041549
MXI1#460139.96157162875930.001011470541259020.00723788776009257
MYC#460935.22228187160940.007020843755740150.0296250616543067
NFKB1#479035.488063424193840.006049381815655430.0270945787565502
NR2C2#7182332.61461090524092.88098172333076e-050.000606626714118834
NR3C1#2908314.9730233311730.0002978331194675480.00310464049945816
PAX5#507936.669565531177830.003370290999677260.0173744914218517
REST#597839.650028716128020.001112636247114590.00771751457876075
RXRA#6256320.07461713913330.0001235730348432220.0016607700663996
SIN3A#2594235.408884726815140.006318961977991520.0278458257392176
SIX5#147912317.0867153554590.0002004060546325010.00240383690591062
SP1#666735.69838137814090.005403962701712170.0248037470600385
SRF#6722313.79717826216780.0003806615025800190.00376690417547419
TAF7#6879311.43306940492390.0006690181981945830.0054604244764961
TCF12#6938310.63446490218640.0008313523990202070.00632240684491891
YY1#752834.911170749853860.008441455341808260.0331410102414523
ZBTB7A#5134137.35190930787590.002516255860282270.0141045108304004
ZNF143#7702313.50087655222790.0004062804962997170.00390605990546314



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.