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Coexpression cluster:C3093: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189155233371077!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114935125629791!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00658434440274814!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278274376759442!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323612703684295!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320435739213367!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319079091611752!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460108476379565!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401750801302765!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00759927986527292!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00894827714039407!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108306469034149!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127617564417516!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185755977700877!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293217859401666!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00199007600215337!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00244938569121071!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469507238593868!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172299095264229!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00879512137869047!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00482976187210706!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275436590158371!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245437904154867!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000937464964061519!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00540550762813276!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.0024735636996621!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00613001998535796!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189527315513567!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327945971224608!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139599068149811
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}}
}}

Revision as of 15:55, 26 November 2012


Full id: C3093_mesenchymal_gastric_oral_glioma_liver_osteosarcoma_maxillary



Phase1 CAGE Peaks


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
embryonic cell4.04e-11250
epithelial cell5.62e-10253
animal cell3.61e-09679
eukaryotic cell3.61e-09679
endodermal cell3.04e-0758
Uber Anatomy
Ontology termp-valuen
epithelial tube4.33e-11117
trunk2.76e-09199
subdivision of trunk1.04e-08112
immaterial anatomical entity3.85e-08117
artery2.51e-0742
arterial blood vessel2.51e-0742
arterial system2.51e-0742
organism subdivision8.86e-07264
Disease
Ontology termp-valuen
cancer5.24e-12235
disease of cellular proliferation2.06e-11239
organ system cancer4.48e-09137
cell type cancer2.34e-08143


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#90536.336201576962630.003930750035764890.0189155233371077
CEBPB#105137.971147625824820.001974187055288560.0114935125629791
CHD2#1106310.34402283411690.0009033701102746880.00658434440274814
CTCF#1066435.360256373075030.0064925092527670.0278274376759442
E2F1#186934.907389214879320.008460985347239390.0323612703684295
E2F6#187635.017155731697390.00791769806886330.0320435739213367
EGR1#195834.988179094810140.008056488137383440.0319079091611752
ELF1#199734.258097958807540.01295179875054610.0460108476379565
ELK4#2005210.8237877723120.01091284719516480.0401750801302765
ETS1#211339.728760922202340.001085840092584840.00759927986527292
FOS#235338.99795530889440.001372499272417130.00894827714039407
HMGN3#932438.178547723350590.001827766942164210.0108306469034149
IRF1#365937.63716375356390.002244692747297240.0127617564417516
MAX#414936.452555509007120.003721913834265510.0185755977700877
MYC#460935.22228187160940.007020843755740150.0293217859401666
NFYA#4800318.42558069983050.0001598135507814160.00199007600215337
NFYB#4801316.75979325353650.0002123649923296180.00244938569121071
NRF1#4899312.21027944771090.0005492172401020010.00469507238593868
PAX5#507936.669565531177830.003370290999677260.0172299095264229
POU2F2#545239.106124057742520.001324165192682130.00879512137869047
RFX5#5993312.04791082719510.0005717246050312580.00482976187210706
SIN3A#2594235.408884726815140.006318961977991520.0275436590158371
SP1#666735.69838137814090.005403962701712170.0245437904154867
SP2#6668326.15353049384465.58768218891694e-050.000937464964061519
TAF7#6879311.43306940492390.0006690181981945830.00540550762813276
TFAP2A#7020316.5186343730450.0002218033880766340.0024735636996621
TFAP2C#7022310.80922860986020.0007916746575753130.00613001998535796
USF1#739136.361499277207960.00388404057290560.0189527315513567
YY1#752834.911170749853860.008441455341808260.0327945971224608
ZBTB7A#5134137.35190930787590.002516255860282270.0139599068149811



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.