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Coexpression cluster:C4551: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190950092090446!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281007531641!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.0017223507416202!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327328807482714!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324001437432025!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00918560077796609!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322170067228315!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464580611934429!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000678984869582728!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764745117199189!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154719884545334!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128639961498561!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295808415768011!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173582119398014!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278035924342541!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109361252737751!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000648713359365185!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191017759179548!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330974642205621!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243689463922175!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109993179102081
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190950092090446!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281007531641!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.0017223507416202!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327328807482714!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324001437432025!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00918560077796609!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322170067228315!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464580611934429!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000678984869582728!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764745117199189!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154719884545334!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128639961498561!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295808415768011!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173582119398014!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278035924342541!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109361252737751!THAP1#55145;3:31.3691446028513:3.23800758564397e-05:0.000648713359365185!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191017759179548!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330974642205621!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00243689463922175!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109993179102081
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}}
}}

Revision as of 16:48, 26 November 2012


Full id: C4551_osteoclastoma_Mesothelial_Preadipocyte_Mallassezderived_hepatic_rectal_Smooth



Phase1 CAGE Peaks

Hg19::chr6:117803797..117803844,+p1@DCBLD1
Hg19::chr6:117803847..117803869,+p2@DCBLD1
Hg19::chr6:117803876..117803888,+p3@DCBLD1


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 epithelium2.61e-24148
trunk mesenchyme9.07e-21122
trunk6.28e-17199
multi-cellular organism3.00e-16656
organism subdivision5.20e-16264
mesenchyme6.78e-16160
entire embryonic mesenchyme6.78e-16160
epithelial vesicle9.84e-1678
anatomical group9.92e-16625
multilaminar epithelium1.68e-1583
anatomical system1.97e-15624
epithelial tube5.49e-15117
somite1.32e-1471
presomitic mesoderm1.32e-1471
presumptive segmental plate1.32e-1471
dermomyotome1.32e-1471
trunk paraxial mesoderm1.32e-1471
paraxial mesoderm5.50e-1472
presumptive paraxial mesoderm5.50e-1472
skeletal muscle tissue5.62e-1462
striated muscle tissue5.62e-1462
myotome5.62e-1462
cell layer5.67e-14309
muscle tissue8.79e-1464
musculature8.79e-1464
musculature of body8.79e-1464
dense mesenchyme tissue9.13e-1473
epithelium1.04e-13306
vasculature2.61e-1378
vascular system2.61e-1378
epithelial tube open at both ends3.48e-1359
blood vessel3.48e-1359
blood vasculature3.48e-1359
vascular cord3.48e-1359
vessel6.12e-1368
embryonic structure3.47e-12564
splanchnic layer of lateral plate mesoderm8.20e-1283
multi-tissue structure1.23e-11342
germ layer2.96e-11560
germ layer / neural crest2.96e-11560
embryonic tissue2.96e-11560
presumptive structure2.96e-11560
germ layer / neural crest derived structure2.96e-11560
epiblast (generic)2.96e-11560
artery6.89e-1142
arterial blood vessel6.89e-1142
arterial system6.89e-1142
developing anatomical structure1.12e-10581
anatomical cluster2.48e-10373
embryo1.14e-09592
anatomical conduit1.66e-09240
endoderm-derived structure1.95e-09160
endoderm1.95e-09160
presumptive endoderm1.95e-09160
systemic artery4.59e-0933
systemic arterial system4.59e-0933
surface structure1.43e-0799
digestive system2.19e-07145
digestive tract2.19e-07145
primitive gut2.19e-07145
simple squamous epithelium2.82e-0722
mesoderm3.78e-07315
mesoderm-derived structure3.78e-07315
presumptive mesoderm3.78e-07315
tube6.47e-07192


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#90536.336201576962630.003930750035764890.0190950092090446
CTCF#1066435.360256373075030.0064925092527670.0281007531641
CTCFL#140690319.74647435897440.0001298372005551160.0017223507416202
E2F1#186934.907389214879320.008460985347239390.0327328807482714
E2F6#187635.017155731697390.00791769806886330.0324001437432025
EBF1#187938.9064668465690.00141523283560980.00918560077796609
EGR1#195834.988179094810140.008056488137383440.0322170067228315
ELF1#199734.258097958807540.01295179875054610.0464580611934429
ESR1#2099330.76860329615453.43136389821584e-050.000678984869582728
ETS1#211339.728760922202340.001085840092584840.00764745117199189
GABPB1#255337.067683836182170.002832212825417420.0154719884545334
IRF1#365937.63716375356390.002244692747297240.0128639961498561
MYC#460935.22228187160940.007020843755740150.0295808415768011
PAX5#507936.669565531177830.003370290999677260.0173582119398014
SIN3A#2594235.408884726815140.006318961977991520.0278035924342541
SPI1#668838.204323508522730.001810593189410520.0109361252737751
THAP1#55145331.36914460285133.23800758564397e-050.000648713359365185
USF1#739136.361499277207960.00388404057290560.0191017759179548
YY1#752834.911170749853860.008441455341808260.0330974642205621
ZEB1#6935316.88843201754390.0002075486917327580.00243689463922175
ZNF263#1012738.221841637010680.001799043925565870.0109993179102081



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.