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Coexpression cluster:C3084: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.0012925643645697!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189137803725063!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278262957095262!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171083363471812!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00435426962488013!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320423322592325!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460077177547799!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166857602458575!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000673624462717601!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00759877066667567!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00579410346109131!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.00084868868830523!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108294180332835!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127610617731738!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156153195383379!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185747101322146!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.0071817915465736!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293206134439278!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.004694688110903!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172282228826437!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027541360070923!SIX5#147912;3:17.086715355459:0.000200406054632501:0.0023898387690984!SMARCC2#6601;3:94.1553744268976:1.19621075407887e-06:4.84416653529441e-05!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308031616514183!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00627715537892361!USF1#7391;3:6.36149927720796:0.0038840405729056:0.018951846075205!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00420428475823583!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00387679568323857
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}}
}}

Revision as of 15:55, 26 November 2012


Full id: C3084_Mallassezderived_Mesothelial_leiomyoma_granulosa_Sertoli_acute_Prostate



Phase1 CAGE Peaks

Hg19::chr11:114310081..114310082,+p6@REXO2
Hg19::chr11:114310102..114310118,+p3@REXO2
Hg19::chr11:114310124..114310140,+p4@REXO2


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><br>

Uber Anatomy
Ontology termp-valuen
unilaminar epithelium2.60e-13148
trunk8.07e-13199
mesenchyme8.23e-13160
entire embryonic mesenchyme8.23e-13160
splanchnic layer of lateral plate mesoderm9.23e-1383
organism subdivision5.72e-12264
trunk mesenchyme8.69e-12122
multilaminar epithelium1.39e-1183
somite2.22e-1171
presomitic mesoderm2.22e-1171
presumptive segmental plate2.22e-1171
dermomyotome2.22e-1171
trunk paraxial mesoderm2.22e-1171
artery3.17e-1142
arterial blood vessel3.17e-1142
arterial system3.17e-1142
epithelial tube3.31e-11117
dense mesenchyme tissue3.74e-1173
paraxial mesoderm4.97e-1172
presumptive paraxial mesoderm4.97e-1172
skeletal muscle tissue5.03e-1162
striated muscle tissue5.03e-1162
myotome5.03e-1162
vasculature6.03e-1178
vascular system6.03e-1178
epithelial vesicle1.39e-1078
muscle tissue2.73e-1064
musculature2.73e-1064
musculature of body2.73e-1064
vessel5.27e-1068
epithelial tube open at both ends5.88e-1059
blood vessel5.88e-1059
blood vasculature5.88e-1059
vascular cord5.88e-1059
primordium1.53e-08160
cell layer2.86e-08309
systemic artery3.69e-0833
systemic arterial system3.69e-0833
epithelium5.30e-08306
cardiovascular system9.58e-08109
reproductive structure1.03e-0759
reproductive system1.03e-0759
circulatory system1.42e-07112
multi-tissue structure2.74e-07342


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
ATF3#467322.46317452600878.81932387510763e-050.0012925643645697
CCNT2#90536.336201576962630.003930750035764890.0189137803725063
CTCF#1066435.360256373075030.0064925092527670.0278262957095262
CTCFL#140690319.74647435897440.0001298372005551160.00171083363471812
E2F4#1874312.66806031528440.0004917987006298980.00435426962488013
E2F6#187635.017155731697390.00791769806886330.0320423322592325
ELF1#199734.258097958807540.01295179875054610.0460077177547799
EP300#203336.77394172622320.003216880500103790.0166857602458575
ESR1#2099330.76860329615453.43136389821584e-050.000673624462717601
ETS1#211339.728760922202340.001085840092584840.00759877066667567
FOXA1#3169311.08141974938550.000734755275698670.00579410346109131
GATA3#2625327.2365163572064.94721007899563e-050.00084868868830523
HMGN3#932438.178547723350590.001827766942164210.0108294180332835
IRF1#365937.63716375356390.002244692747297240.0127610617731738
JUND#372736.994663941871030.002921845042734990.0156153195383379
MAX#414936.452555509007120.003721913834265510.0185747101322146
MXI1#460139.96157162875930.001011470541259020.0071817915465736
MYC#460935.22228187160940.007020843755740150.0293206134439278
NRF1#4899312.21027944771090.0005492172401020010.004694688110903
PAX5#507936.669565531177830.003370290999677260.0172282228826437
SIN3A#2594235.408884726815140.006318961977991520.027541360070923
SIX5#147912317.0867153554590.0002004060546325010.0023898387690984
SMARCC2#6601394.15537442689761.19621075407887e-064.84416653529441e-05
SMC3#9126315.04493284493280.0002935825420371870.00308031616514183
TCF12#6938310.63446490218640.0008313523990202070.00627715537892361
USF1#739136.361499277207960.00388404057290560.018951846075205
USF2#7392312.99219738506960.0004558979393427810.00420428475823583
ZNF143#7702313.50087655222790.0004062804962997170.00387679568323857



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.

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