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Coexpression cluster:C2870: Difference between revisions

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|full_id=C2870_Smooth_leiomyoma_giant_Synoviocyte_Urothelial_Myoblast_mesenchymal
|full_id=C2870_Smooth_leiomyoma_giant_Synoviocyte_Urothelial_Myoblast_mesenchymal
|id=C2870
|id=C2870
|ontology_enrichment_celltype=CL:0000055!5.39e-28!180;CL:0000220!1.52e-25!246;CL:0002321!1.28e-24!248;CL:0000222!3.00e-19!119;CL:0000057!6.70e-16!75;CL:0000680!1.64e-15!57;CL:0000056!1.64e-15!57;CL:0000355!1.64e-15!57;CL:0000359!2.59e-14!32;CL:0000192!3.66e-14!42;CL:0000514!3.66e-14!42;CL:0000187!7.38e-14!54;CL:0000183!2.98e-13!59;CL:0002371!3.02e-12!591;CL:0000548!8.94e-12!679;CL:0000004!8.94e-12!679;CL:0000255!8.94e-12!679;CL:0000012!4.14e-11!682;CL:0000393!6.90e-11!60;CL:0000211!6.90e-11!60;CL:0000144!2.36e-10!625;CL:0000066!2.97e-10!254;CL:0002620!5.38e-08!23;CL:0000499!2.82e-07!27
|ontology_enrichment_celltype=CL:0002321!3.00e-25!250;CL:0000222!2.64e-19!121;CL:0000057!4.14e-16!76;CL:0000680!2.34e-15!58;CL:0000056!2.34e-15!58;CL:0000355!2.34e-15!58;CL:0000359!2.38e-14!32;CL:0000192!3.82e-14!43;CL:0000514!3.82e-14!43;CL:0002371!4.47e-14!588;CL:0000187!9.75e-14!55;CL:0000548!1.34e-13!679;CL:0000255!1.34e-13!679;CL:0000183!4.89e-13!59;CL:0000055!2.25e-11!106;CL:0000066!4.23e-11!253;CL:0000393!3.11e-10!61;CL:0000211!3.11e-10!61;CL:0002620!4.88e-08!23;CL:0000499!1.18e-07!28;CL:0000003!7.69e-07!722
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!1.32e-22!83;UBERON:0002329!1.32e-22!83;UBERON:0003077!1.32e-22!83;UBERON:0003059!1.32e-22!83;UBERON:0007282!1.32e-22!83;UBERON:0009618!1.32e-22!83;UBERON:0007285!1.32e-22!83;UBERON:0005256!1.50e-21!143;UBERON:0000486!4.15e-21!82;UBERON:0002049!4.14e-18!79;UBERON:0007798!4.14e-18!79;UBERON:0000475!5.70e-18!365;UBERON:0004290!1.22e-17!70;UBERON:0002100!9.96e-17!216;UBERON:0000119!3.84e-16!312;UBERON:0000055!1.05e-15!69;UBERON:0000483!2.30e-15!309;UBERON:0001981!3.83e-15!60;UBERON:0007500!3.83e-15!60;UBERON:0004537!3.83e-15!60;UBERON:0006965!3.83e-15!60;UBERON:0001637!4.05e-15!42;UBERON:0003509!4.05e-15!42;UBERON:0004572!4.05e-15!42;UBERON:0003914!9.34e-15!118;UBERON:0000490!1.11e-14!138;UBERON:0000481!3.95e-14!347;UBERON:0003102!5.29e-14!95;UBERON:0001134!6.16e-14!61;UBERON:0002036!6.16e-14!61;UBERON:0003082!6.16e-14!61;UBERON:0004872!9.51e-14!84;UBERON:0002385!1.18e-13!63;UBERON:0001015!1.18e-13!63;UBERON:0000383!1.18e-13!63;UBERON:0000467!1.92e-13!625;UBERON:0000480!3.00e-13!626;UBERON:0004573!6.92e-13!33;UBERON:0004571!6.92e-13!33;UBERON:0000468!1.08e-12!659;UBERON:0000477!1.33e-12!286;UBERON:0003104!1.74e-12!238;UBERON:0009142!1.74e-12!238;UBERON:0004535!6.92e-12!110;UBERON:0001009!5.40e-11!113;UBERON:0004111!6.58e-10!241;UBERON:0002199!1.68e-08!45;UBERON:0002416!1.68e-08!45;UBERON:0000923!3.45e-08!604;UBERON:0005291!3.45e-08!604;UBERON:0006598!3.45e-08!604;UBERON:0002532!3.45e-08!604;UBERON:0002050!3.96e-08!605;UBERON:0005423!3.96e-08!605;UBERON:0002097!8.01e-08!40;UBERON:0000947!2.30e-07!21;UBERON:0010191!2.30e-07!21;UBERON:0000922!3.30e-07!612;UBERON:0003100!7.23e-07!41
|ontology_enrichment_uberon=UBERON:0000486!4.42e-21!83;UBERON:0000475!6.39e-18!264;UBERON:0000490!7.15e-18!148;UBERON:0002049!8.61e-18!78;UBERON:0007798!8.61e-18!78;UBERON:0002329!2.06e-17!71;UBERON:0003059!2.06e-17!71;UBERON:0007282!2.06e-17!71;UBERON:0004290!2.06e-17!71;UBERON:0009618!2.06e-17!71;UBERON:0007524!2.66e-17!73;UBERON:0007503!3.34e-17!78;UBERON:0003077!4.62e-17!72;UBERON:0007285!4.62e-17!72;UBERON:0000119!1.44e-16!309;UBERON:0003102!4.06e-16!99;UBERON:0000483!9.63e-16!306;UBERON:0005256!2.26e-15!122;UBERON:0000055!2.49e-15!68;UBERON:0001637!4.34e-15!42;UBERON:0003509!4.34e-15!42;UBERON:0004572!4.34e-15!42;UBERON:0007500!7.13e-15!59;UBERON:0001981!7.13e-15!59;UBERON:0004537!7.13e-15!59;UBERON:0006965!7.13e-15!59;UBERON:0003914!1.03e-14!117;UBERON:0000467!7.12e-14!624;UBERON:0001134!1.05e-13!62;UBERON:0002036!1.05e-13!62;UBERON:0003082!1.05e-13!62;UBERON:0000480!1.42e-13!625;UBERON:0003104!1.82e-13!160;UBERON:0009142!1.82e-13!160;UBERON:0002385!2.00e-13!64;UBERON:0001015!2.00e-13!64;UBERON:0000383!2.00e-13!64;UBERON:0004872!2.42e-13!83;UBERON:0002100!4.55e-13!199;UBERON:0004573!7.43e-13!33;UBERON:0004571!7.43e-13!33;UBERON:0000468!1.73e-12!656;UBERON:0000481!7.29e-12!342;UBERON:0004535!1.73e-11!109;UBERON:0001009!2.15e-10!112;UBERON:0004111!1.41e-09!240;UBERON:0002199!3.15e-09!46;UBERON:0002416!3.15e-09!46;UBERON:0002097!1.23e-08!41;UBERON:0000477!1.25e-08!373;UBERON:0004923!1.42e-07!66;UBERON:0000947!3.60e-07!21;UBERON:0010191!3.60e-07!21;UBERON:0000033!4.17e-07!56;UBERON:0000075!6.24e-07!16;UBERON:0003100!6.77e-07!41
|tf_chipseq_enrich=EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240630413501147!RXRA#6256;3:15.05596285435:0.000475830799730358:0.00434095849869313!SMARCB1#6598;3:13.6895368358681:0.000630578340937934:0.00518313956785903!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.0157208580600629!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279957236827587
|tf_chipseq_enrich=EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240630413501147!RXRA#6256;3:15.05596285435:0.000475830799730358:0.00434095849869313!SMARCB1#6598;3:13.6895368358681:0.000630578340937934:0.00518313956785903!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.0157208580600629!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279957236827587
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}}
}}

Revision as of 14:31, 19 October 2012


Full id: C2870_Smooth_leiomyoma_giant_Synoviocyte_Urothelial_Myoblast_mesenchymal



Phase1 CAGE Peaks

Hg19::chr6:86159765..86159820,+p1@NT5E
Hg19::chr6:86159821..86159839,+p2@NT5E
Hg19::chr6:86159843..86159854,+p4@NT5E
Hg19::chr6:86203923..86203945,+p@chr6:86203923..86203945
+


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
multilaminar epithelium4.42e-2183
organism subdivision6.39e-18264
unilaminar epithelium7.15e-18148
vasculature8.61e-1878
vascular system8.61e-1878
somite2.06e-1771
presomitic mesoderm2.06e-1771
presumptive segmental plate2.06e-1771
dermomyotome2.06e-1771
trunk paraxial mesoderm2.06e-1771
dense mesenchyme tissue2.66e-1773
epithelial vesicle3.34e-1778
paraxial mesoderm4.62e-1772
presumptive paraxial mesoderm4.62e-1772
cell layer1.44e-16309
surface structure4.06e-1699
epithelium9.63e-16306
trunk mesenchyme2.26e-15122
vessel2.49e-1568
artery4.34e-1542
arterial blood vessel4.34e-1542
arterial system4.34e-1542
epithelial tube open at both ends7.13e-1559
blood vessel7.13e-1559
blood vasculature7.13e-1559
vascular cord7.13e-1559
epithelial tube1.03e-14117
anatomical system7.12e-14624
skeletal muscle tissue1.05e-1362
striated muscle tissue1.05e-1362
myotome1.05e-1362
anatomical group1.42e-13625
mesenchyme1.82e-13160
entire embryonic mesenchyme1.82e-13160
muscle tissue2.00e-1364
musculature2.00e-1364
musculature of body2.00e-1364
splanchnic layer of lateral plate mesoderm2.42e-1383
trunk4.55e-13199
systemic artery7.43e-1333
systemic arterial system7.43e-1333
multi-cellular organism1.73e-12656
multi-tissue structure7.29e-12342
cardiovascular system1.73e-11109
circulatory system2.15e-10112
anatomical conduit1.41e-09240
integument3.15e-0946
integumental system3.15e-0946
skin of body1.23e-0841
anatomical cluster1.25e-08373
organ component layer1.42e-0766
aorta3.60e-0721
aortic system3.60e-0721
head4.17e-0756
subdivision of skeletal system6.24e-0716
female organism6.77e-0741


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
EBF1#187936.679850134926750.005184294118278910.0240630413501147
RXRA#6256315.055962854350.0004758307997303580.00434095849869313
SMARCB1#6598313.68953683586810.0006305783409379340.00518313956785903
TFAP2C#702238.106921457395170.002947011739866440.0157208580600629
ZNF263#1012736.166381227758010.006539814347975980.0279957236827587



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:C2870&oldid=2249035"