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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1935_heart_pineal_mature_neuroblastoma_putamen_neuroectodermal_occipital
|full_id=C1935_heart_pineal_mature_neuroblastoma_putamen_neuroectodermal_occipital
|id=C1935
|id=C1935

Revision as of 14:34, 12 September 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 organism1.30e-31115
regional part of nervous system2.37e-3094
nervous system2.37e-3094
central nervous system3.85e-2982
brain1.98e-2669
future brain1.98e-2669
neural tube1.01e-2457
neural rod1.01e-2457
future spinal cord1.01e-2457
neural keel1.01e-2457
neurectoderm1.92e-2490
ectoderm4.68e-24173
presumptive ectoderm4.68e-24173
regional part of brain2.05e-2359
neural plate2.17e-2386
presumptive neural plate2.17e-2386
ectoderm-derived structure5.53e-23169
anterior region of body1.95e-21129
craniocervical region1.95e-21129
head2.31e-21123
anterior neural tube5.15e-2042
regional part of forebrain1.78e-1941
forebrain1.78e-1941
future forebrain1.78e-1941
pre-chordal neural plate1.06e-1761
organism subdivision3.93e-17365
multi-tissue structure2.85e-16347
telencephalon8.45e-1634
gray matter8.88e-1634
brain grey matter8.88e-1634
cerebral hemisphere1.13e-1532
regional part of telencephalon2.53e-1533
multi-cellular organism6.67e-15659
organ9.11e-13511
cerebral cortex1.93e-1225
pallium1.93e-1225
regional part of cerebral cortex4.76e-1222
neocortex3.53e-1120
organ part1.77e-10219
anatomical system1.92e-09625
anatomical group3.12e-09626
embryo4.70e-09612
anatomical cluster4.81e-09286
embryonic structure7.96e-08605
developing anatomical structure7.96e-08605
germ layer1.45e-07604
embryonic tissue1.45e-07604
presumptive structure1.45e-07604
epiblast (generic)1.45e-07604


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.