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Coexpression cluster:C4660: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!1.87e-30!365;UBERON:0000481!3.32e-29!347;UBERON:0005743!1.20e-26!86;UBERON:0001017!1.49e-26!82;UBERON:0000073!2.67e-26!94;UBERON:0001016!2.67e-26!94;UBERON:0004121!8.58e-25!169;UBERON:0000477!2.31e-24!286;UBERON:0000119!5.01e-24!312;UBERON:0000033!1.03e-23!123;UBERON:0000924!1.31e-23!173;UBERON:0006601!1.31e-23!173;UBERON:0000483!3.62e-23!309;UBERON:0000153!5.92e-23!129;UBERON:0007811!5.92e-23!129;UBERON:0003075!6.23e-23!86;UBERON:0007284!6.23e-23!86;UBERON:0001049!1.81e-22!57;UBERON:0005068!1.81e-22!57;UBERON:0006241!1.81e-22!57;UBERON:0007135!1.81e-22!57;UBERON:0000955!4.00e-22!69;UBERON:0006238!4.00e-22!69;UBERON:0002616!4.74e-22!59;UBERON:0002346!3.98e-21!90;UBERON:0004111!2.39e-19!241;UBERON:0000025!8.63e-19!194;UBERON:0003056!1.60e-18!61;UBERON:0002780!4.19e-18!41;UBERON:0001890!4.19e-18!41;UBERON:0006240!4.19e-18!41;UBERON:0003080!5.40e-18!42;UBERON:0000468!6.21e-17!659;UBERON:0001893!8.14e-16!34;UBERON:0001869!1.55e-15!32;UBERON:0002020!1.93e-15!34;UBERON:0003528!1.93e-15!34;UBERON:0002791!3.32e-15!33;UBERON:0000467!5.41e-15!625;UBERON:0000480!7.77e-15!626;UBERON:0007023!9.91e-15!115;UBERON:0000922!8.62e-14!612;UBERON:0002619!4.84e-13!22;UBERON:0000956!1.92e-12!25;UBERON:0000203!1.92e-12!25;UBERON:0001950!6.49e-12!20;UBERON:0002050!8.58e-12!605;UBERON:0005423!8.58e-12!605;UBERON:0000923!1.47e-11!604;UBERON:0005291!1.47e-11!604;UBERON:0006598!1.47e-11!604;UBERON:0002532!1.47e-11!604;UBERON:0000064!3.90e-10!219;UBERON:0000914!1.09e-09!83;UBERON:0002329!1.09e-09!83;UBERON:0003077!1.09e-09!83;UBERON:0003059!1.09e-09!83;UBERON:0007282!1.09e-09!83;UBERON:0009618!1.09e-09!83;UBERON:0007285!1.09e-09!83;UBERON:0000062!2.26e-09!511;UBERON:0001048!5.96e-09!168;UBERON:0004290!6.72e-09!70;UBERON:0003104!7.53e-08!238;UBERON:0009142!7.53e-08!238;UBERON:0002100!4.47e-07!216
|ontology_enrichment_uberon=UBERON:0000475!1.87e-30!365;UBERON:0000481!3.32e-29!347;UBERON:0005743!1.20e-26!86;UBERON:0001017!1.49e-26!82;UBERON:0000073!2.67e-26!94;UBERON:0001016!2.67e-26!94;UBERON:0004121!8.58e-25!169;UBERON:0000477!2.31e-24!286;UBERON:0000119!5.01e-24!312;UBERON:0000033!1.03e-23!123;UBERON:0000924!1.31e-23!173;UBERON:0006601!1.31e-23!173;UBERON:0000483!3.62e-23!309;UBERON:0000153!5.92e-23!129;UBERON:0007811!5.92e-23!129;UBERON:0003075!6.23e-23!86;UBERON:0007284!6.23e-23!86;UBERON:0001049!1.81e-22!57;UBERON:0005068!1.81e-22!57;UBERON:0006241!1.81e-22!57;UBERON:0007135!1.81e-22!57;UBERON:0000955!4.00e-22!69;UBERON:0006238!4.00e-22!69;UBERON:0002616!4.74e-22!59;UBERON:0002346!3.98e-21!90;UBERON:0004111!2.39e-19!241;UBERON:0000025!8.63e-19!194;UBERON:0003056!1.60e-18!61;UBERON:0002780!4.19e-18!41;UBERON:0001890!4.19e-18!41;UBERON:0006240!4.19e-18!41;UBERON:0003080!5.40e-18!42;UBERON:0000468!6.21e-17!659;UBERON:0001893!8.14e-16!34;UBERON:0001869!1.55e-15!32;UBERON:0002020!1.93e-15!34;UBERON:0003528!1.93e-15!34;UBERON:0002791!3.32e-15!33;UBERON:0000467!5.41e-15!625;UBERON:0000480!7.77e-15!626;UBERON:0007023!9.91e-15!115;UBERON:0000922!8.62e-14!612;UBERON:0002619!4.84e-13!22;UBERON:0000956!1.92e-12!25;UBERON:0000203!1.92e-12!25;UBERON:0001950!6.49e-12!20;UBERON:0002050!8.58e-12!605;UBERON:0005423!8.58e-12!605;UBERON:0000923!1.47e-11!604;UBERON:0005291!1.47e-11!604;UBERON:0006598!1.47e-11!604;UBERON:0002532!1.47e-11!604;UBERON:0000064!3.90e-10!219;UBERON:0000914!1.09e-09!83;UBERON:0002329!1.09e-09!83;UBERON:0003077!1.09e-09!83;UBERON:0003059!1.09e-09!83;UBERON:0007282!1.09e-09!83;UBERON:0009618!1.09e-09!83;UBERON:0007285!1.09e-09!83;UBERON:0000062!2.26e-09!511;UBERON:0001048!5.96e-09!168;UBERON:0004290!6.72e-09!70;UBERON:0003104!7.53e-08!238;UBERON:0009142!7.53e-08!238;UBERON:0002100!4.47e-07!216
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115787118474354!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281228971776257!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.00172322625349801!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168430231388349!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438944429473236!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00668417919012863!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247841410769417!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109411874158911
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}}
}}

Revision as of 14:17, 5 September 2012


Full id: C4660_lung_cerebellum_rhabdomyosarcoma_mesenchymal_Neural_myxofibrosarcoma_Fibroblast



Phase1 CAGE Peaks

Hg19::chr7:14029034..14029087,-p5@ETV1
Hg19::chr7:14029283..14029311,-p1@ETV1
Hg19::chr7:14029312..14029325,-p4@ETV1


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
organism subdivision1.87e-30365
multi-tissue structure3.32e-29347
central nervous system1.49e-2682
regional part of nervous system2.67e-2694
nervous system2.67e-2694
ectoderm-derived structure8.58e-25169
anatomical cluster2.31e-24286
cell layer5.01e-24312
head1.03e-23123
ectoderm1.31e-23173
presumptive ectoderm1.31e-23173
epithelium3.62e-23309
anterior region of body5.92e-23129
craniocervical region5.92e-23129
neural plate6.23e-2386
presumptive neural plate6.23e-2386
neural tube1.81e-2257
neural rod1.81e-2257
future spinal cord1.81e-2257
neural keel1.81e-2257
brain4.00e-2269
future brain4.00e-2269
regional part of brain4.74e-2259
neurectoderm3.98e-2190
anatomical conduit2.39e-19241
tube8.63e-19194
pre-chordal neural plate1.60e-1861
regional part of forebrain4.19e-1841
forebrain4.19e-1841
future forebrain4.19e-1841
anterior neural tube5.40e-1842
multi-cellular organism6.21e-17659
telencephalon8.14e-1634
cerebral hemisphere1.55e-1532
gray matter1.93e-1534
brain grey matter1.93e-1534
regional part of telencephalon3.32e-1533
anatomical system5.41e-15625
anatomical group7.77e-15626
adult organism9.91e-15115
embryo8.62e-14612
regional part of cerebral cortex4.84e-1322
cerebral cortex1.92e-1225
pallium1.92e-1225
neocortex6.49e-1220
embryonic structure8.58e-12605
developing anatomical structure8.58e-12605
germ layer1.47e-11604
embryonic tissue1.47e-11604
presumptive structure1.47e-11604
epiblast (generic)1.47e-11604
organ part3.90e-10219
somite1.09e-0983
paraxial mesoderm1.09e-0983
presomitic mesoderm1.09e-0983
presumptive segmental plate1.09e-0983
trunk paraxial mesoderm1.09e-0983
presumptive paraxial mesoderm1.09e-0983
organ2.26e-09511
primordium5.96e-09168
dermomyotome6.72e-0970
mesenchyme7.53e-08238
entire embryonic mesenchyme7.53e-08238
trunk4.47e-07216


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
CEBPB#105137.971147625824820.001974187055288560.0115787118474354
CTCF#1066435.360256373075030.0064925092527670.0281228971776257
CTCFL#140690319.74647435897440.0001298372005551160.00172322625349801
EP300#203336.77394172622320.003216880500103790.0168430231388349
GATA2#2624312.7449317335540.0004829527704283790.00438944429473236
RAD21#5885310.35503389545630.0009004912073565420.00668417919012863
SP1#666735.69838137814090.005403962701712170.0247841410769417
SPI1#668838.204323508522730.001810593189410520.0109411874158911



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.