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Coexpression cluster:C2021: Difference between revisions

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|full_id=C2021_basal_mesenchymal_Dendritic_Smooth_Fibroblast_Aortic_Mallassezderived
|full_id=C2021_basal_mesenchymal_Dendritic_Smooth_Fibroblast_Aortic_Mallassezderived
|id=C2021
|id=C2021
|ontology_enrichment_celltype=CL:0000222!2.74e-19!119;CL:0000055!1.73e-16!180;CL:0002371!3.17e-15!591;CL:0000359!1.05e-14!32;CL:0000192!2.71e-14!42;CL:0000514!2.71e-14!42;CL:0000680!1.08e-13!57;CL:0000056!1.08e-13!57;CL:0000355!1.08e-13!57;CL:0000144!1.51e-13!625;CL:0000187!5.96e-13!54;CL:0000723!3.90e-11!436;CL:0000057!4.61e-11!75;CL:0000048!9.45e-11!430;CL:0000183!1.12e-10!59;CL:0000393!7.18e-10!60;CL:0000211!7.18e-10!60;CL:0000220!3.10e-09!246;CL:0000034!4.19e-09!444;CL:0002620!5.21e-09!23;CL:0002321!1.13e-08!248;CL:0000548!1.68e-07!679;CL:0000004!1.68e-07!679;CL:0000255!1.68e-07!679;CL:0002539!4.39e-07!10;CL:0000012!8.04e-07!682
|ontology_enrichment_celltype=CL:0000359!3.34e-14!32;CL:0002371!8.06e-14!588;CL:0000222!1.03e-13!121;CL:0000723!1.42e-12!433;CL:0000192!2.48e-12!43;CL:0000514!2.48e-12!43;CL:0000048!3.01e-12!427;CL:0000548!2.06e-11!679;CL:0000255!2.06e-11!679;CL:0000034!2.60e-11!441;CL:0002620!4.57e-11!23;CL:0000680!1.34e-10!58;CL:0000056!1.34e-10!58;CL:0000355!1.34e-10!58;CL:0000057!2.73e-10!76;CL:0000187!1.33e-09!55;CL:0002539!2.58e-08!10;CL:0000183!4.67e-08!59;CL:0000393!2.20e-07!61;CL:0000211!2.20e-07!61;CL:0000003!3.90e-07!722;CL:0002321!7.47e-07!250
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:2394!1.17e-07!14
|ontology_enrichment_uberon=UBERON:0004872!2.77e-19!84;UBERON:0000055!2.12e-17!69;UBERON:0002049!2.18e-16!79;UBERON:0007798!2.18e-16!79;UBERON:0001981!4.03e-16!60;UBERON:0007500!4.03e-16!60;UBERON:0004537!4.03e-16!60;UBERON:0006965!4.03e-16!60;UBERON:0000914!4.81e-16!83;UBERON:0002329!4.81e-16!83;UBERON:0003077!4.81e-16!83;UBERON:0003059!4.81e-16!83;UBERON:0007282!4.81e-16!83;UBERON:0009618!4.81e-16!83;UBERON:0007285!4.81e-16!83;UBERON:0001637!9.01e-16!42;UBERON:0003509!9.01e-16!42;UBERON:0004572!9.01e-16!42;UBERON:0003081!1.62e-15!216;UBERON:0000486!4.48e-15!82;UBERON:0004535!1.62e-14!110;UBERON:0001009!7.34e-14!113;UBERON:0004290!7.88e-14!70;UBERON:0002204!8.17e-14!167;UBERON:0004573!4.77e-13!33;UBERON:0004571!4.77e-13!33;UBERON:0001134!5.54e-12!61;UBERON:0002036!5.54e-12!61;UBERON:0003082!5.54e-12!61;UBERON:0002385!1.12e-11!63;UBERON:0001015!1.12e-11!63;UBERON:0000383!1.12e-11!63;UBERON:0000480!3.92e-10!626;UBERON:0000467!4.41e-10!625;UBERON:0003914!9.32e-10!118;UBERON:0005256!3.50e-09!143;UBERON:0000490!8.77e-09!138;UBERON:0000947!1.56e-08!21;UBERON:0010191!1.56e-08!21;UBERON:0000926!3.53e-08!448;UBERON:0004120!3.53e-08!448;UBERON:0006603!3.53e-08!448;UBERON:0000468!5.16e-08!659;UBERON:0003102!7.29e-08!95;UBERON:0002199!7.74e-08!45;UBERON:0002416!7.74e-08!45;UBERON:0002097!1.34e-07!40;UBERON:0004237!4.39e-07!10;UBERON:0004695!4.39e-07!10;UBERON:0002111!4.39e-07!10;UBERON:0004178!4.39e-07!10
|ontology_enrichment_uberon=UBERON:0001637!7.01e-17!42;UBERON:0003509!7.01e-17!42;UBERON:0004572!7.01e-17!42;UBERON:0000055!3.30e-15!68;UBERON:0004872!4.76e-15!83;UBERON:0004573!1.37e-14!33;UBERON:0004571!1.37e-14!33;UBERON:0007500!3.52e-14!59;UBERON:0001981!3.52e-14!59;UBERON:0004537!3.52e-14!59;UBERON:0006965!3.52e-14!59;UBERON:0000926!2.22e-13!315;UBERON:0004120!2.22e-13!315;UBERON:0006603!2.22e-13!315;UBERON:0002049!9.24e-13!78;UBERON:0007798!9.24e-13!78;UBERON:0003081!5.18e-12!203;UBERON:0000486!5.44e-12!83;UBERON:0007524!8.39e-11!73;UBERON:0002329!8.77e-11!71;UBERON:0003059!8.77e-11!71;UBERON:0007282!8.77e-11!71;UBERON:0004290!8.77e-11!71;UBERON:0009618!8.77e-11!71;UBERON:0000947!1.50e-10!21;UBERON:0010191!1.50e-10!21;UBERON:0003077!2.12e-10!72;UBERON:0007285!2.12e-10!72;UBERON:0002204!2.48e-10!167;UBERON:0004535!4.66e-10!109;UBERON:0001009!3.06e-09!112;UBERON:0007503!3.33e-09!78;UBERON:0001134!5.55e-09!62;UBERON:0002036!5.55e-09!62;UBERON:0003082!5.55e-09!62;UBERON:0000490!1.99e-08!148;UBERON:0002097!2.57e-08!41;UBERON:0004237!2.58e-08!10;UBERON:0004695!2.58e-08!10;UBERON:0002111!2.58e-08!10;UBERON:0004178!2.58e-08!10;UBERON:0002385!2.85e-08!64;UBERON:0001015!2.85e-08!64;UBERON:0000383!2.85e-08!64;UBERON:0002199!1.45e-07!46;UBERON:0002416!1.45e-07!46;UBERON:0003914!1.52e-07!117;UBERON:0003102!1.91e-07!99
|tf_chipseq_enrich=BATF#10538;5:24.3578017923036:1.16482472299935e-07:6.74726174405599e-06!BCL11A#53335;5:28.3694551036071:5.43377642717329e-08:3.44564770053158e-06!IRF4#3662;5:21.9145126867441:1.97628413609567e-07:1.07444632425661e-05!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000985886770029043!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00239363752141197!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00117202799079499!REST#5978;5:9.65002871612802:1.19441074361324e-05:0.000301822075132405!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204589095426124!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000575991173307256!SRF#6722;5:13.7971782621678:1.9987012616697e-06:7.32943683523602e-05!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220863029832918!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135594035399265
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}}
}}

Revision as of 11:58, 19 October 2012


Full id: C2021_basal_mesenchymal_Dendritic_Smooth_Fibroblast_Aortic_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr9:5510492..5510552,+p1@PDCD1LG2
Hg19::chr9:5510558..5510567,+p2@PDCD1LG2
Hg19::chr9:5510574..5510587,+p3@PDCD1LG2
Hg19::chr9:5510607..5510612,+p5@PDCD1LG2
Hg19::chr9:5510613..5510622,+p4@PDCD1LG2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
artery7.01e-1742
arterial blood vessel7.01e-1742
arterial system7.01e-1742
vessel3.30e-1568
splanchnic layer of lateral plate mesoderm4.76e-1583
systemic artery1.37e-1433
systemic arterial system1.37e-1433
epithelial tube open at both ends3.52e-1459
blood vessel3.52e-1459
blood vasculature3.52e-1459
vascular cord3.52e-1459
mesoderm2.22e-13315
mesoderm-derived structure2.22e-13315
presumptive mesoderm2.22e-13315
vasculature9.24e-1378
vascular system9.24e-1378
lateral plate mesoderm5.18e-12203
multilaminar epithelium5.44e-1283
dense mesenchyme tissue8.39e-1173
somite8.77e-1171
presomitic mesoderm8.77e-1171
presumptive segmental plate8.77e-1171
dermomyotome8.77e-1171
trunk paraxial mesoderm8.77e-1171
aorta1.50e-1021
aortic system1.50e-1021
paraxial mesoderm2.12e-1072
presumptive paraxial mesoderm2.12e-1072
musculoskeletal system2.48e-10167
cardiovascular system4.66e-10109
circulatory system3.06e-09112
epithelial vesicle3.33e-0978
skeletal muscle tissue5.55e-0962
striated muscle tissue5.55e-0962
myotome5.55e-0962
unilaminar epithelium1.99e-08148
skin of body2.57e-0841
blood vessel smooth muscle2.58e-0810
arterial system smooth muscle2.58e-0810
artery smooth muscle tissue2.58e-0810
aorta smooth muscle tissue2.58e-0810
muscle tissue2.85e-0864
musculature2.85e-0864
musculature of body2.85e-0864
integument1.45e-0746
integumental system1.45e-0746
epithelial tube1.52e-07117
surface structure1.91e-0799
Disease
Ontology termp-valuen
ovarian cancer1.17e-0714


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
BATF#10538524.35780179230361.16482472299935e-076.74726174405599e-06
BCL11A#53335528.36945510360715.43377642717329e-083.44564770053158e-06
IRF4#3662521.91451268674411.97628413609567e-071.07444632425661e-05
JUND#372756.994663941871035.97069468343598e-050.000985886770029043
NFKB1#479055.488063424193840.0002008162847462320.00239363752141197
PAX5#507956.669565531177837.57493746384605e-050.00117202799079499
REST#597859.650028716128021.19441074361324e-050.000301822075132405
SP1#666755.69838137814090.000166391843712550.00204589095426124
SPI1#668858.204323508522732.68916109982495e-050.000575991173307256
SRF#6722513.79717826216781.9987012616697e-067.32943683523602e-05
STAT3#6774510.51946499715427.759040745861e-060.000220863029832918
TAF1#687253.343046285745290.002394600090870310.0135594035399265



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2021&oldid=2248083"