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Coexpression cluster:C1935: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239430141067298!EBF1#1879;4:7.1251734772552:0.000723053104677421:0.00577331370026033!EP300#2033;4:5.41915338097856:0.0020938692794389:0.012124729079359!GATA2#2624;4:10.1959453868432:0.000177544777760982:0.00215787257588493!MAX#4149;4:5.1620444072057:0.00252630900948518:0.0140030350621814!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256898683766985!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386860440265291!REST#5978;4:7.72002297290242:0.000528636377365057:0.00457455088372104!SMC3#9126;4:12.0359462759463:9.2360978468394e-05:0.00134384065620794!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714345372854528!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135520558627075!TAF7#6879;4:9.14645552393913:0.000272066287241299:0.00290356948428306!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00353072034995847
|tf_chipseq_enrich=CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239430141067298!EBF1#1879;4:7.1251734772552:0.000723053104677421:0.00577331370026033!EP300#2033;4:5.41915338097856:0.0020938692794389:0.012124729079359!GATA2#2624;4:10.1959453868432:0.000177544777760982:0.00215787257588493!MAX#4149;4:5.1620444072057:0.00252630900948518:0.0140030350621814!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256898683766985!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386860440265291!REST#5978;4:7.72002297290242:0.000528636377365057:0.00457455088372104!SMC3#9126;4:12.0359462759463:9.2360978468394e-05:0.00134384065620794!SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714345372854528!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135520558627075!TAF7#6879;4:9.14645552393913:0.000272066287241299:0.00290356948428306!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00353072034995847
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}}
}}

Revision as of 15:12, 26 November 2012


Full id: C1935_heart_pineal_mature_neuroblastoma_putamen_neuroectodermal_occipital



Phase1 CAGE Peaks

Hg19::chr4:142053952..142053977,-p2@RNF150
Hg19::chr4:142054469..142054497,-p4@RNF150
Hg19::chr4:142054498..142054547,-p3@RNF150
Hg19::chr4:142054563..142054577,-p6@RNF150
Hg19::chr4:142054590..142054648,-p1@RNF150


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
adult organism3.02e-37114
central nervous system2.55e-3181
nervous system2.68e-3089
brain2.10e-2968
future brain2.10e-2968
neural tube1.43e-2656
neural rod1.43e-2656
future spinal cord1.43e-2656
neural keel1.43e-2656
organ system subdivision2.60e-26223
regional part of nervous system1.68e-2553
regional part of brain1.68e-2553
neurectoderm5.20e-2586
neural plate3.07e-2482
presumptive neural plate3.07e-2482
ectoderm-derived structure5.47e-24171
ectoderm5.47e-24171
presumptive ectoderm5.47e-24171
regional part of forebrain2.51e-2241
forebrain2.51e-2241
anterior neural tube2.51e-2241
future forebrain2.51e-2241
structure with developmental contribution from neural crest5.75e-21132
pre-chordal neural plate7.55e-1861
telencephalon8.06e-1834
brain grey matter9.78e-1834
gray matter9.78e-1834
cerebral hemisphere1.22e-1732
ecto-epithelium3.32e-17104
regional part of telencephalon5.68e-1732
anatomical cluster5.63e-16373
multi-tissue structure3.06e-15342
cerebral cortex1.08e-1325
pallium1.08e-1325
regional part of cerebral cortex4.74e-1322
multi-cellular organism2.67e-12656
neocortex4.90e-1220
organ9.77e-12503
anatomical system3.60e-09624
anatomical group4.95e-09625
organ part1.02e-08218
embryo6.56e-08592
developing anatomical structure2.57e-07581
germ layer5.52e-07560
germ layer / neural crest5.52e-07560
embryonic tissue5.52e-07560
presumptive structure5.52e-07560
germ layer / neural crest derived structure5.52e-07560
epiblast (generic)5.52e-07560
embryonic structure7.50e-07564


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#1066444.288205098460020.005152015588243280.0239430141067298
EBF1#187947.12517347725520.0007230531046774210.00577331370026033
EP300#203345.419153380978560.00209386927943890.012124729079359
GATA2#2624410.19594538684320.0001775447777609820.00215787257588493
MAX#414945.16204440720570.002526309009485180.0140030350621814
MYC#460944.177825497287520.005691969036823440.0256898683766985
RAD21#588548.284027116365060.0004011622639122450.00386860440265291
REST#597847.720022972902420.0005286363773650570.00457455088372104
SMC3#9126412.03594627594639.2360978468394e-050.00134384065620794
SPI1#668846.563458806818180.0009957429636454020.00714345372854528
TAF1#687253.343046285745290.002394600090870310.0135520558627075
TAF7#687949.146455523939130.0002720662872412990.00290356948428306
YY1#752854.911170749853860.00034993140821360.00353072034995847



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.