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Coexpression cluster:C4680: Difference between revisions

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|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285782876353647!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115806628772906!CTCF#10664;3:5.36025637307503:0.006492509252767:0.028127563523032!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168472461413268!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187394763986335!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00723293199990079!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296035326822135!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00668512945728674!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165991565093136!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310779111167867!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376405100056378!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645542489329335!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191170796641542!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423193715109952
|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285782876353647!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115806628772906!CTCF#10664;3:5.36025637307503:0.006492509252767:0.028127563523032!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168472461413268!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187394763986335!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00723293199990079!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296035326822135!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00668512945728674!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00165991565093136!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310779111167867!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376405100056378!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645542489329335!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191170796641542!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423193715109952
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}}
}}

Revision as of 16:53, 26 November 2012


Full id: C4680_Smooth_clear_gastric_Mesothelial_glioma_rectum_melanoma



Phase1 CAGE Peaks

Hg19::chr7:27183263..27183284,-p2@HOXA5
Hg19::chr7:27183291..27183324,-p1@HOXA5
Hg19::chr7:27183325..27183338,-p5@HOXA5


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
subdivision of trunk4.38e-19112
trunk2.15e-14199
cavitated compound organ2.17e-1331
epithelial tube1.53e-12117
kidney1.01e-1126
kidney mesenchyme1.01e-1126
upper urinary tract1.01e-1126
kidney rudiment1.01e-1126
kidney field1.01e-1126
abdominal segment of trunk1.26e-1160
abdomen1.26e-1160
trunk region element2.56e-10101
excretory tube6.36e-1016
kidney epithelium6.36e-1016
abdomen element2.07e-0954
abdominal segment element2.07e-0954
mesenchyme3.46e-09160
entire embryonic mesenchyme3.46e-09160
nephron epithelium3.87e-0915
renal tubule3.87e-0915
nephron tubule3.87e-0915
nephron3.87e-0915
uriniferous tubule3.87e-0915
nephrogenic mesenchyme3.87e-0915
renal system5.11e-0948
urinary system structure9.51e-0947
simple squamous epithelium1.53e-0822
blood vessel endothelium1.55e-0818
endothelium1.55e-0818
cardiovascular system endothelium1.55e-0818
epithelial tube open at both ends1.63e-0859
blood vessel1.63e-0859
blood vasculature1.63e-0859
vascular cord1.63e-0859
thoracic segment of trunk3.69e-0852
nephron tubule epithelium6.68e-0810
vessel9.43e-0868
compound organ1.13e-0768
cortex of kidney2.88e-0712
renal parenchyma2.88e-0712
organism subdivision3.61e-07264
squamous epithelium9.64e-0725


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285782876353647
CEBPB#105137.971147625824820.001974187055288560.0115806628772906
CTCF#1066435.360256373075030.0064925092527670.028127563523032
EP300#203336.77394172622320.003216880500103790.0168472461413268
MAX#414936.452555509007120.003721913834265510.0187394763986335
MXI1#460139.96157162875930.001011470541259020.00723293199990079
MYC#460935.22228187160940.007020843755740150.0296035326822135
RAD21#5885310.35503389545630.0009004912073565420.00668512945728674
RXRA#6256320.07461713913330.0001235730348432220.00165991565093136
SMC3#9126315.04493284493280.0002935825420371870.00310779111167867
SRF#6722313.79717826216780.0003806615025800190.00376405100056378
STAT3#6774310.51946499715420.0008589184530415310.00645542489329335
USF1#739136.361499277207960.00388404057290560.0191170796641542
USF2#7392312.99219738506960.0004558979393427810.00423193715109952



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.