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Coexpression cluster:C3433: Difference between revisions

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|tf_chipseq_enrich=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00659354748388973!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129337343256811!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278858025106816!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.031974598692008!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461033711557015!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293828852336504!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662858762370382!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612519604003685!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189891074521902!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109130712982618
|tf_chipseq_enrich=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00659354748388973!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129337343256811!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278858025106816!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.031974598692008!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461033711557015!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293828852336504!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00662858762370382!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00612519604003685!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189891074521902!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109130712982618
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}}
}}

Revision as of 16:08, 26 November 2012


Full id: C3433_teratocarcinoma_Saos2_signet_rectal_tubular_gastric_Wilms



Phase1 CAGE Peaks

Hg19::chr14:54423434..54423446,-p6@BMP4
Hg19::chr14:54423459..54423483,-p4@BMP4
Hg19::chr14:54423533..54423552,-p1@BMP4


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
anatomical cluster1.51e-22373
anatomical conduit1.74e-17240
cell layer2.36e-14309
multi-tissue structure3.11e-14342
squamous epithelium4.00e-1425
epithelium5.82e-14306
epithelial tube1.33e-13117
simple squamous epithelium1.10e-1222
tube2.08e-12192
blood vessel endothelium1.09e-1018
endothelium1.09e-1018
cardiovascular system endothelium1.09e-1018
digestive system1.10e-10145
digestive tract1.10e-10145
primitive gut1.10e-10145
organism subdivision1.92e-10264
subdivision of digestive tract1.55e-09118
intermediate mesoderm2.00e-0928
endoderm-derived structure6.63e-09160
endoderm6.63e-09160
presumptive endoderm6.63e-09160
subdivision of trunk8.39e-09112
vasculature1.98e-0878
vascular system1.98e-0878
unilaminar epithelium2.11e-08148
immaterial anatomical entity2.89e-08117
primordium3.16e-08160
duct4.03e-0819
endothelial tube5.00e-089
arterial system endothelium5.00e-089
endothelium of artery5.00e-089
gastrointestinal system7.91e-0825
mesenchyme9.48e-08160
entire embryonic mesenchyme9.48e-08160
trunk1.29e-07199
trunk region element3.03e-07101
multi-cellular organism3.17e-07656
abdomen element4.39e-0754
abdominal segment element4.39e-0754
splanchnic layer of lateral plate mesoderm8.64e-0783


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#1106310.34402283411690.0009033701102746880.00659354748388973
CTBP2#1488362.71700033932814.049570681927e-060.000129337343256811
CTCF#1066435.360256373075030.0064925092527670.0278858025106816
EGR1#195834.988179094810140.008056488137383440.031974598692008
ELF1#199734.258097958807540.01295179875054610.0461033711557015
MYC#460935.22228187160940.007020843755740150.0293828852336504
RAD21#5885310.35503389545630.0009004912073565420.00662858762370382
TCF7L2#6934310.77017656313730.0008003181298398380.00612519604003685
USF1#739136.361499277207960.00388404057290560.0189891074521902
ZNF263#1012738.221841637010680.001799043925565870.0109130712982618



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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