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Coexpression cluster:C3212: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!5.05e-08!14
|ontology_enrichment_disease=DOID:2394!5.05e-08!14
|ontology_enrichment_uberon=UBERON:0004290!1.69e-23!70;UBERON:0000914!1.74e-22!83;UBERON:0002329!1.74e-22!83;UBERON:0003077!1.74e-22!83;UBERON:0003059!1.74e-22!83;UBERON:0007282!1.74e-22!83;UBERON:0009618!1.74e-22!83;UBERON:0007285!1.74e-22!83;UBERON:0001134!7.25e-21!61;UBERON:0002036!7.25e-21!61;UBERON:0003082!7.25e-21!61;UBERON:0002385!1.68e-20!63;UBERON:0001015!1.68e-20!63;UBERON:0000383!1.68e-20!63;UBERON:0002049!1.72e-20!79;UBERON:0007798!1.72e-20!79;UBERON:0004872!8.95e-20!84;UBERON:0000486!6.16e-19!82;UBERON:0000490!1.16e-17!138;UBERON:0001637!1.32e-17!42;UBERON:0003509!1.32e-17!42;UBERON:0004572!1.32e-17!42;UBERON:0001009!8.35e-17!113;UBERON:0004535!1.30e-16!110;UBERON:0001981!3.72e-16!60;UBERON:0007500!3.72e-16!60;UBERON:0004537!3.72e-16!60;UBERON:0006965!3.72e-16!60;UBERON:0000119!4.38e-16!312;UBERON:0000475!4.32e-15!365;UBERON:0000055!5.41e-15!69;UBERON:0000483!7.44e-15!309;UBERON:0004573!4.87e-14!33;UBERON:0004571!4.87e-14!33;UBERON:0005256!1.10e-13!143;UBERON:0003914!1.23e-13!118;UBERON:0002100!2.22e-11!216;UBERON:0000948!2.25e-10!24;UBERON:0005498!2.25e-10!24;UBERON:0004140!2.25e-10!24;UBERON:0009881!2.25e-10!24;UBERON:0004141!2.25e-10!24;UBERON:0003084!2.25e-10!24;UBERON:0007005!2.25e-10!24;UBERON:0004139!2.25e-10!24;UBERON:0004291!2.25e-10!24;UBERON:0002199!2.96e-10!45;UBERON:0002416!2.96e-10!45;UBERON:0007100!3.33e-10!27;UBERON:0000481!9.79e-10!347;UBERON:0000477!4.67e-09!286;UBERON:0003102!7.45e-09!95;UBERON:0002097!1.18e-08!40;UBERON:0000947!3.25e-08!21;UBERON:0010191!3.25e-08!21;UBERON:0000025!1.63e-07!194;UBERON:0004111!1.63e-07!241;UBERON:0003104!2.28e-07!238;UBERON:0009142!2.28e-07!238;UBERON:0000468!2.37e-07!659
|ontology_enrichment_uberon=UBERON:0004290!1.69e-23!70;UBERON:0000914!1.74e-22!83;UBERON:0002329!1.74e-22!83;UBERON:0003077!1.74e-22!83;UBERON:0003059!1.74e-22!83;UBERON:0007282!1.74e-22!83;UBERON:0009618!1.74e-22!83;UBERON:0007285!1.74e-22!83;UBERON:0001134!7.25e-21!61;UBERON:0002036!7.25e-21!61;UBERON:0003082!7.25e-21!61;UBERON:0002385!1.68e-20!63;UBERON:0001015!1.68e-20!63;UBERON:0000383!1.68e-20!63;UBERON:0002049!1.72e-20!79;UBERON:0007798!1.72e-20!79;UBERON:0004872!8.95e-20!84;UBERON:0000486!6.16e-19!82;UBERON:0000490!1.16e-17!138;UBERON:0001637!1.32e-17!42;UBERON:0003509!1.32e-17!42;UBERON:0004572!1.32e-17!42;UBERON:0001009!8.35e-17!113;UBERON:0004535!1.30e-16!110;UBERON:0001981!3.72e-16!60;UBERON:0007500!3.72e-16!60;UBERON:0004537!3.72e-16!60;UBERON:0006965!3.72e-16!60;UBERON:0000119!4.38e-16!312;UBERON:0000475!4.32e-15!365;UBERON:0000055!5.41e-15!69;UBERON:0000483!7.44e-15!309;UBERON:0004573!4.87e-14!33;UBERON:0004571!4.87e-14!33;UBERON:0005256!1.10e-13!143;UBERON:0003914!1.23e-13!118;UBERON:0002100!2.22e-11!216;UBERON:0000948!2.25e-10!24;UBERON:0005498!2.25e-10!24;UBERON:0004140!2.25e-10!24;UBERON:0009881!2.25e-10!24;UBERON:0004141!2.25e-10!24;UBERON:0003084!2.25e-10!24;UBERON:0007005!2.25e-10!24;UBERON:0004139!2.25e-10!24;UBERON:0004291!2.25e-10!24;UBERON:0002199!2.96e-10!45;UBERON:0002416!2.96e-10!45;UBERON:0007100!3.33e-10!27;UBERON:0000481!9.79e-10!347;UBERON:0000477!4.67e-09!286;UBERON:0003102!7.45e-09!95;UBERON:0002097!1.18e-08!40;UBERON:0000947!3.25e-08!21;UBERON:0010191!3.25e-08!21;UBERON:0000025!1.63e-07!194;UBERON:0004111!1.63e-07!241;UBERON:0003104!2.28e-07!238;UBERON:0009142!2.28e-07!238;UBERON:0000468!2.37e-07!659
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278502967038951!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166998599537896!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00895107103234498!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436060382041752!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443267639792363
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0935776,0.327622,0.225752,0.00177054,0.0958756,0.000113015,0.316866,0.171683,0.158847,0.0406636,0.071111,0.270604,0.101021,0.00220393,0.175934,0.000734859,0.215705,0.252796,0.205954,0.0750181
}}
}}

Revision as of 14:01, 5 September 2012


Full id: C3212_Meningeal_mesenchymal_Fibroblast_alveolar_Smooth_Chondrocyte_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:94528216..94528229,+p@chr11:94528216..94528229
+
Hg19::chr11:94528241..94528266,+p@chr11:94528241..94528266
+
Hg19::chr11:94528267..94528294,+p@chr11:94528267..94528294
+


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
dermomyotome1.69e-2370
somite1.74e-2283
paraxial mesoderm1.74e-2283
presomitic mesoderm1.74e-2283
presumptive segmental plate1.74e-2283
trunk paraxial mesoderm1.74e-2283
presumptive paraxial mesoderm1.74e-2283
skeletal muscle tissue7.25e-2161
striated muscle tissue7.25e-2161
myotome7.25e-2161
muscle tissue1.68e-2063
musculature1.68e-2063
musculature of body1.68e-2063
vasculature1.72e-2079
vascular system1.72e-2079
splanchnic layer of lateral plate mesoderm8.95e-2084
multilaminar epithelium6.16e-1982
unilaminar epithelium1.16e-17138
artery1.32e-1742
arterial blood vessel1.32e-1742
arterial system1.32e-1742
circulatory system8.35e-17113
cardiovascular system1.30e-16110
blood vessel3.72e-1660
epithelial tube open at both ends3.72e-1660
blood vasculature3.72e-1660
vascular cord3.72e-1660
cell layer4.38e-16312
organism subdivision4.32e-15365
vessel5.41e-1569
epithelium7.44e-15309
systemic artery4.87e-1433
systemic arterial system4.87e-1433
trunk mesenchyme1.10e-13143
epithelial tube1.23e-13118
trunk2.22e-11216
heart2.25e-1024
primitive heart tube2.25e-1024
primary heart field2.25e-1024
anterior lateral plate mesoderm2.25e-1024
heart tube2.25e-1024
heart primordium2.25e-1024
cardiac mesoderm2.25e-1024
cardiogenic plate2.25e-1024
heart rudiment2.25e-1024
integument2.96e-1045
integumental system2.96e-1045
primary circulatory organ3.33e-1027
multi-tissue structure9.79e-10347
anatomical cluster4.67e-09286
surface structure7.45e-0995
skin of body1.18e-0840
aorta3.25e-0821
aortic system3.25e-0821
tube1.63e-07194
anatomical conduit1.63e-07241
mesenchyme2.28e-07238
entire embryonic mesenchyme2.28e-07238
multi-cellular organism2.37e-07659
Disease
Ontology termp-valuen
ovarian cancer5.05e-0814


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
CTCF#1066435.360256373075030.0064925092527670.0278502967038951
EP300#203336.77394172622320.003216880500103790.0166998599537896
FOS#235338.99795530889440.001372499272417130.00895107103234498
GATA2#2624312.7449317335540.0004829527704283790.00436060382041752
JUN#3725312.51282919233630.0005103313992726250.00443267639792363



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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