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Coexpression cluster:C4660: Difference between revisions

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|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
|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 16:52, 26 November 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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.60e-09106
electrically responsive cell1.81e-0761
electrically active cell1.81e-0761
fibroblast7.98e-0776
Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest5.95e-28132
central nervous system2.08e-2781
anatomical cluster2.89e-26373
nervous system5.85e-2689
multi-tissue structure9.17e-26342
neural plate1.07e-2382
presumptive neural plate1.07e-2382
ectoderm-derived structure1.21e-23171
ectoderm1.21e-23171
presumptive ectoderm1.21e-23171
neural tube1.31e-2356
neural rod1.31e-2356
future spinal cord1.31e-2356
neural keel1.31e-2356
regional part of nervous system1.42e-2253
regional part of brain1.42e-2253
brain3.00e-2268
future brain3.00e-2268
neurectoderm1.32e-2186
cell layer1.52e-20309
organ system subdivision4.17e-20223
epithelium4.26e-20306
regional part of forebrain3.49e-1941
forebrain3.49e-1941
anterior neural tube3.49e-1941
future forebrain3.49e-1941
ecto-epithelium1.26e-18104
pre-chordal neural plate7.87e-1861
multi-cellular organism5.52e-17656
anatomical conduit7.75e-17240
telencephalon9.65e-1734
brain grey matter1.56e-1634
gray matter1.56e-1634
tube2.27e-16192
cerebral hemisphere2.77e-1632
adult organism3.48e-16114
regional part of telencephalon7.55e-1632
anatomical system1.52e-15624
anatomical group2.71e-15625
regional part of cerebral cortex2.23e-1322
cerebral cortex6.50e-1325
pallium6.50e-1325
neocortex2.83e-1220
embryo3.62e-12592
germ layer5.43e-10560
germ layer / neural crest5.43e-10560
embryonic tissue5.43e-10560
presumptive structure5.43e-10560
germ layer / neural crest derived structure5.43e-10560
epiblast (generic)5.43e-10560
organ part1.14e-09218
embryonic structure1.25e-09564
developing anatomical structure1.42e-09581
organ6.81e-09503
dense mesenchyme tissue9.41e-0973
paraxial mesoderm1.63e-0872
presumptive paraxial mesoderm1.63e-0872
somite4.15e-0871
presomitic mesoderm4.15e-0871
presumptive segmental plate4.15e-0871
dermomyotome4.15e-0871
trunk paraxial mesoderm4.15e-0871
organism subdivision5.42e-08264
epithelial vesicle4.87e-0778
primordium7.00e-07160


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.

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