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Coexpression cluster:C3923: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115262814102908!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462578794100364!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167573336600499!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00434162139296285!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128161746028306!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444450475388873!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156867616520948!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000857987927700755!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186665846588962!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00720628773167003!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294702745470739!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00664357171553474!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484898051200743!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203189795593456!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309243238606371!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246714661918219!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064295143575978!WRNIP1#56897;3:109.819964349376:7.53682839543883e-07:3.3240659661792e-05!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140299634718926!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109480450146938
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115262814102908!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462578794100364!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167573336600499!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00434162139296285!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128161746028306!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444450475388873!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156867616520948!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000857987927700755!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186665846588962!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00720628773167003!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294702745470739!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00664357171553474!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00484898051200743!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203189795593456!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309243238606371!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246714661918219!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064295143575978!WRNIP1#56897;3:109.819964349376:7.53682839543883e-07:3.3240659661792e-05!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140299634718926!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109480450146938
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}}
}}

Revision as of 16:26, 26 November 2012


Full id: C3923_mesenchymal_Mesothelial_Fibroblast_leiomyoma_basal_mature_epithelioid



Phase1 CAGE Peaks

Hg19::chr1:203596195..203596206,+p5@ATP2B4
Hg19::chr1:203596211..203596216,+p6@ATP2B4
Hg19::chr1:203596217..203596249,+p3@ATP2B4


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
splanchnic layer of lateral plate mesoderm1.47e-1583
epithelial tube open at both ends4.10e-1459
blood vessel4.10e-1459
blood vasculature4.10e-1459
vascular cord4.10e-1459
vasculature1.09e-1278
vascular system1.09e-1278
vessel2.23e-1268
artery6.62e-1242
arterial blood vessel6.62e-1242
arterial system6.62e-1242
dense mesenchyme tissue1.01e-1173
epithelial vesicle1.42e-1178
muscle tissue1.84e-1164
musculature1.84e-1164
musculature of body1.84e-1164
paraxial mesoderm1.93e-1172
presumptive paraxial mesoderm1.93e-1172
systemic artery3.15e-1133
systemic arterial system3.15e-1133
somite3.25e-1171
presomitic mesoderm3.25e-1171
presumptive segmental plate3.25e-1171
dermomyotome3.25e-1171
trunk paraxial mesoderm3.25e-1171
skeletal muscle tissue4.45e-1162
striated muscle tissue4.45e-1162
myotome4.45e-1162
circulatory system4.59e-10112
multilaminar epithelium1.53e-0983
cardiovascular system2.72e-09109
aorta3.99e-0921
aortic system3.99e-0921
epithelial tube5.16e-09117
multi-cellular organism5.76e-08656
trunk mesenchyme6.49e-08122
epithelium8.96e-08306
anatomical cluster9.41e-08373
mesenchyme9.81e-08160
entire embryonic mesenchyme9.81e-08160
cell layer1.31e-07309
unilaminar epithelium2.31e-07148
anatomical system2.75e-07624
anatomical group3.56e-07625
tube3.82e-07192
anatomical conduit8.47e-07240


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#105137.971147625824820.001974187055288560.0115262814102908
ELF1#199734.258097958807540.01295179875054610.0462578794100364
EP300#203336.77394172622320.003216880500103790.0167573336600499
GTF2F1#2962312.73966087675770.0004835525047438590.00434162139296285
IRF1#365937.63716375356390.002244692747297240.0128161746028306
JUN#3725312.51282919233630.0005103313992726250.00444450475388873
JUND#372736.994663941871030.002921845042734990.0156867616520948
MAFK#7975327.10073313782995.02195559325033e-050.000857987927700755
MAX#414936.452555509007120.003721913834265510.0186665846588962
MXI1#460139.96157162875930.001011470541259020.00720628773167003
MYC#460935.22228187160940.007020843755740150.0294702745470739
RAD21#5885310.35503389545630.0009004912073565420.00664357171553474
RFX5#5993312.04791082719510.0005717246050312580.00484898051200743
SMARCB1#6598318.25271578115740.000164397760679890.00203189795593456
SMC3#9126315.04493284493280.0002935825420371870.00309243238606371
SP1#666735.69838137814090.005403962701712170.0246714661918219
STAT3#6774310.51946499715420.0008589184530415310.0064295143575978
WRNIP1#568973109.8199643493767.53682839543883e-073.3240659661792e-05
ZBTB7A#5134137.35190930787590.002516255860282270.0140299634718926
ZNF263#1012738.221841637010680.001799043925565870.0109480450146938



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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