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Coexpression cluster:C2570: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512495548001119!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817758032799834!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106547825895324!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160984131646375!FOS#2353;4:8.9979553088944:0.000152514771116863:0.0019501089839219!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.00030410337286313!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.0006140618335194!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186197524939798!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.002482198318833!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000743749984688214!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391936406332028!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129485418885656!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796830747208026!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438272391048537!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322458882469629!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244453068144892!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106915974118007!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249099616557403
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512495548001119!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817758032799834!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106547825895324!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160984131646375!FOS#2353;4:8.9979553088944:0.000152514771116863:0.0019501089839219!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.00030410337286313!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.0006140618335194!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186197524939798!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.002482198318833!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000743749984688214!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391936406332028!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129485418885656!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796830747208026!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438272391048537!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322458882469629!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244453068144892!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106915974118007!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249099616557403
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}}
}}

Revision as of 15:35, 26 November 2012


Full id: C2570_mesenchymal_leiomyoma_Fibroblast_CD14_Mesothelial_Gingival_meningioma



Phase1 CAGE Peaks

Hg19::chr1:223900193..223900249,+p1@CAPN2
Hg19::chr1:223900250..223900274,+p3@CAPN2
Hg19::chr1:223900286..223900299,+p4@CAPN2
Hg19::chr1:223900302..223900328,+p2@CAPN2


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
animal cell5.31e-22679
eukaryotic cell5.31e-22679
somatic cell1.45e-21588
mesodermal cell6.67e-17121
native cell1.10e-15722
fibroblast5.95e-1476
classical monocyte2.15e-1342
CD14-positive, CD16-negative classical monocyte2.15e-1342
muscle precursor cell3.31e-1358
myoblast3.31e-1358
multi-potent skeletal muscle stem cell3.31e-1358
vascular associated smooth muscle cell7.65e-1332
muscle cell5.51e-1255
embryonic cell6.36e-12250
smooth muscle cell6.79e-1243
smooth muscle myoblast6.79e-1243
contractile cell4.49e-1159
defensive cell1.92e-0948
phagocyte1.92e-0948
electrically responsive cell1.53e-0861
electrically active cell1.53e-0861
multi fate stem cell5.47e-07427
non-terminally differentiated cell6.09e-07106
somatic stem cell6.19e-07433
squamous epithelial cell6.65e-0763
stuff accumulating cell7.30e-0787
Uber Anatomy
Ontology termp-valuen
mesoderm2.44e-20315
mesoderm-derived structure2.44e-20315
presumptive mesoderm2.44e-20315
multilaminar epithelium6.02e-1683
musculoskeletal system9.40e-16167
somite5.21e-1571
presomitic mesoderm5.21e-1571
presumptive segmental plate5.21e-1571
dermomyotome5.21e-1571
trunk paraxial mesoderm5.21e-1571
artery1.10e-1442
arterial blood vessel1.10e-1442
arterial system1.10e-1442
epithelial vesicle1.34e-1478
paraxial mesoderm2.12e-1472
presumptive paraxial mesoderm2.12e-1472
vasculature2.49e-1478
vascular system2.49e-1478
dense mesenchyme tissue2.54e-1473
anatomical group4.50e-14625
anatomical system5.22e-14624
epithelial tube open at both ends1.00e-1359
blood vessel1.00e-1359
blood vasculature1.00e-1359
vascular cord1.00e-1359
unilaminar epithelium1.27e-12148
splanchnic layer of lateral plate mesoderm2.15e-1283
vessel2.41e-1268
lateral plate mesoderm3.03e-12203
multi-cellular organism6.68e-12656
skeletal muscle tissue7.98e-1262
striated muscle tissue7.98e-1262
myotome7.98e-1262
systemic artery3.07e-1133
systemic arterial system3.07e-1133
surface structure3.63e-1199
muscle tissue3.86e-1164
musculature3.86e-1164
musculature of body3.86e-1164
organism subdivision1.88e-10264
cardiovascular system5.16e-10109
circulatory system1.45e-09112
trunk mesenchyme3.41e-09122
epithelial tube1.54e-08117
developing anatomical structure1.67e-08581
embryonic structure2.48e-08564
trunk5.23e-08199
germ layer1.03e-07560
germ layer / neural crest1.03e-07560
embryonic tissue1.03e-07560
presumptive structure1.03e-07560
germ layer / neural crest derived structure1.03e-07560
epiblast (generic)1.03e-07560
aorta1.19e-0721
aortic system1.19e-0721
mesenchyme1.37e-07160
entire embryonic mesenchyme1.37e-07160
embryo1.77e-07592
organ component layer4.27e-0766


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
CCNT2#90546.336201576962630.0006203100587215640.00512495548001119
CTCF#1066445.360256373075030.001211145381643620.00817758032799834
E2F1#186944.907389214879320.001724022357361790.0106547825895324
ELF1#199744.258097958807540.003041525565781240.0160984131646375
FOS#235348.99795530889440.0001525147711168630.0019501089839219
FOSL2#2355416.93020060456171.2165416097647e-050.00030410337286313
GATA1#2623413.56030814380042.95627390049268e-050.0006140618335194
HEY1#2346244.040111043105710.00375304636917980.0186197524939798
HMGN3#932448.178547723350590.0002234570284440470.002482198318833
JUN#3725412.51282919233634.07770316866756e-050.000743749984688214
JUND#372746.994663941871030.000417684217818580.00391936406332028
RAD21#5885410.35503389545638.6948481184721e-050.00129485418885656
SIN3A#2594245.408884726815140.001168172384885160.00796830747208026
SMC3#9126415.04493284493281.95092670935632e-050.000438272391048537
TAF1#687243.343046285745290.008005664898701650.0322458882469629
TBP#690843.706770687096390.005296377814784350.0244453068144892
YY1#752844.911170749853860.00171871838055440.0106915974118007
ZNF263#1012748.221841637010680.0002187871180958320.00249099616557403



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.