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Coexpression cluster:C2894: Difference between revisions

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|tf_chipseq_enrich=CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129355220398119!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819931370412124!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00200086478773575!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435403332126118!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.00154841580172489!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186623058492011!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486640616044611!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0089000525472513!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129948660939483!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323344278890673!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245048687634901
|tf_chipseq_enrich=CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129355220398119!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819931370412124!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00200086478773575!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435403332126118!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.00154841580172489!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186623058492011!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486640616044611!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0089000525472513!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129948660939483!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323344278890673!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245048687634901
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}}
}}

Revision as of 15:47, 26 November 2012


Full id: C2894_Preadipocyte_Adipocyte_tenocyte_pons_mesenchymal_Mesothelial_Smooth



Phase1 CAGE Peaks

Hg19::chr7:37960416..37960421,+p11@EPDR1
Hg19::chr7:37960422..37960438,+p4@EPDR1
Hg19::chr7:37960439..37960448,+p10@EPDR1
Hg19::chr7:37960465..37960476,+p6@EPDR1


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
fat cell1.92e-1015
Uber Anatomy
Ontology termp-valuen
adult organism2.22e-16114
structure with developmental contribution from neural crest1.78e-13132
neural tube1.45e-1256
neural rod1.45e-1256
future spinal cord1.45e-1256
neural keel1.45e-1256
neural plate2.01e-1282
presumptive neural plate2.01e-1282
tube2.15e-12192
regional part of nervous system7.69e-1253
regional part of brain7.69e-1253
neurectoderm8.80e-1186
brain2.10e-1068
future brain2.10e-1068
anatomical conduit5.26e-10240
central nervous system4.59e-0981
cell layer1.08e-08309
multi-tissue structure1.97e-08342
primary circulatory organ3.05e-0827
posterior neural tube3.14e-0815
chordal neural plate3.14e-0815
epithelium4.03e-08306
tissue4.78e-08773
segmental subdivision of hindbrain1.13e-0712
hindbrain1.13e-0712
presumptive hindbrain1.13e-0712
anatomical cluster1.31e-07373
nervous system2.25e-0789
heart2.63e-0724
primitive heart tube2.63e-0724
primary heart field2.63e-0724
anterior lateral plate mesoderm2.63e-0724
heart tube2.63e-0724
heart primordium2.63e-0724
cardiac mesoderm2.63e-0724
cardiogenic plate2.63e-0724
heart rudiment2.63e-0724
ecto-epithelium3.82e-07104
regional part of forebrain8.89e-0741
forebrain8.89e-0741
anterior neural tube8.89e-0741
future forebrain8.89e-0741


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
CHD2#1106410.34402283411698.73193255208051e-050.00129355220398119
CTCF#1066445.360256373075030.001211145381643620.00819931370412124
EBF1#187948.9064668465690.00015887907472010.00200086478773575
EP300#203346.77394172622320.0004748459821442640.00435403332126118
ETS1#211349.728760922202340.0001115955317418140.00154841580172489
HEY1#2346244.040111043105710.00375304636917980.0186623058492011
MAX#414946.452555509007120.0005767613195645490.00486640616044611
MYC#460945.22228187160940.001344309395272740.0089000525472513
RAD21#5885410.35503389545638.6948481184721e-050.00129948660939483
TAF1#687243.343046285745290.008005664898701650.0323344278890673
TBP#690843.706770687096390.005296377814784350.0245048687634901



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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