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Coexpression cluster:C3164: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278434350531653!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171191357010173!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032054753212157!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268641630855191!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172358153812209!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00879679973020348!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662018873751301!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000300947817532743!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308093519974093!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108820016175891!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328055799078333!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.013963615610628!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00387785859559917
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278434350531653!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00171191357010173!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032054753212157!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268641630855191!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172358153812209!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00879679973020348!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662018873751301!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000300947817532743!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00308093519974093!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108820016175891!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0328055799078333!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.013963615610628!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00387785859559917
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}}
}}

Revision as of 15:57, 26 November 2012


Full id: C3164_pharyngeal_temporal_occipital_Hepatocyte_rectum_optic_brain



Phase1 CAGE Peaks

Hg19::chr11:58939589..58939610,+p3@DTX4
Hg19::chr11:58939616..58939668,+p1@DTX4
Hg19::chr11:58939673..58939697,+p2@DTX4


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
organ system subdivision1.63e-21223
adult organism5.23e-20114
neural tube2.62e-1756
neural rod2.62e-1756
future spinal cord2.62e-1756
neural keel2.62e-1756
regional part of nervous system5.99e-1653
regional part of brain5.99e-1653
central nervous system7.69e-1581
neural plate3.23e-1482
presumptive neural plate3.23e-1482
neurectoderm4.80e-1386
subdivision of digestive tract4.98e-13118
regional part of forebrain5.63e-1341
forebrain5.63e-1341
anterior neural tube5.63e-1341
future forebrain5.63e-1341
endoderm-derived structure2.25e-12160
endoderm2.25e-12160
presumptive endoderm2.25e-12160
telencephalon3.57e-1234
nervous system5.84e-1289
brain grey matter8.82e-1234
gray matter8.82e-1234
ecto-epithelium1.25e-11104
digestive system1.56e-11145
digestive tract1.56e-11145
primitive gut1.56e-11145
cerebral hemisphere2.30e-1132
organ part3.05e-11218
pre-chordal neural plate4.13e-1161
regional part of telencephalon5.00e-1132
brain9.72e-1168
future brain9.72e-1168
regional part of cerebral cortex1.41e-1022
cerebral cortex3.80e-1025
pallium3.80e-1025
neocortex5.48e-1020
multi-tissue structure8.86e-10342
ectoderm-derived structure1.08e-09171
ectoderm1.08e-09171
presumptive ectoderm1.08e-09171
anatomical cluster3.69e-09373
gastrointestinal system3.95e-0925
organ2.35e-08503
intestine1.20e-0717


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#1066435.360256373075030.0064925092527670.0278434350531653
CTCFL#140690319.74647435897440.0001298372005551160.00171191357010173
E2F6#187635.017155731697390.00791769806886330.032054753212157
NFKB1#479035.488063424193840.006049381815655430.0268641630855191
PAX5#507936.669565531177830.003370290999677260.0172358153812209
POU2F2#545239.106124057742520.001324165192682130.00879679973020348
RAD21#5885310.35503389545630.0009004912073565420.00662018873751301
SMARCC1#6599343.66335931963151.20046018043203e-050.000300947817532743
SMC3#9126315.04493284493280.0002935825420371870.00308093519974093
SPI1#668838.204323508522730.001810593189410520.0108820016175891
YY1#752834.911170749853860.008441455341808260.0328055799078333
ZBTB7A#5134137.35190930787590.002516255860282270.013963615610628
ZNF143#7702313.50087655222790.0004062804962997170.00387785859559917



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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