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Coexpression cluster:C2716: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!2.16e-19!118;UBERON:0002100!1.96e-18!216;UBERON:0005256!5.05e-18!143;UBERON:0000468!2.27e-17!659;UBERON:0004872!8.25e-17!84;UBERON:0000475!2.78e-14!365;UBERON:0000467!4.86e-14!625;UBERON:0000480!7.79e-14!626;UBERON:0000486!1.53e-13!82;UBERON:0003104!2.68e-13!238;UBERON:0009142!2.68e-13!238;UBERON:0000914!2.86e-13!83;UBERON:0002329!2.86e-13!83;UBERON:0003077!2.86e-13!83;UBERON:0003059!2.86e-13!83;UBERON:0007282!2.86e-13!83;UBERON:0009618!2.86e-13!83;UBERON:0007285!2.86e-13!83;UBERON:0000490!4.28e-13!138;UBERON:0001981!6.48e-13!60;UBERON:0007500!6.48e-13!60;UBERON:0004537!6.48e-13!60;UBERON:0006965!6.48e-13!60;UBERON:0004290!6.62e-13!70;UBERON:0000926!7.40e-13!448;UBERON:0004120!7.40e-13!448;UBERON:0006603!7.40e-13!448;UBERON:0002049!1.12e-12!79;UBERON:0007798!1.12e-12!79;UBERON:0001637!1.21e-12!42;UBERON:0003509!1.21e-12!42;UBERON:0004572!1.21e-12!42;UBERON:0000055!2.51e-12!69;UBERON:0000119!4.69e-12!312;UBERON:0000483!6.64e-12!309;UBERON:0001134!1.95e-11!61;UBERON:0002036!1.95e-11!61;UBERON:0003082!1.95e-11!61;UBERON:0002385!2.64e-11!63;UBERON:0001015!2.64e-11!63;UBERON:0000383!2.64e-11!63;UBERON:0001009!3.59e-11!113;UBERON:0004573!6.91e-11!33;UBERON:0004571!6.91e-11!33;UBERON:0004535!7.01e-11!110;UBERON:0000481!2.14e-10!347;UBERON:0000477!6.16e-10!286;UBERON:0000922!8.19e-09!612;UBERON:0002050!9.54e-09!605;UBERON:0005423!9.54e-09!605;UBERON:0000923!9.59e-09!604;UBERON:0005291!9.59e-09!604;UBERON:0006598!9.59e-09!604;UBERON:0002532!9.59e-09!604;UBERON:0001048!1.33e-08!168;UBERON:0004111!1.90e-08!241;UBERON:0004923!6.15e-08!57;UBERON:0003102!1.00e-07!95;UBERON:0009569!2.25e-07!113;UBERON:0001013!2.70e-07!14;UBERON:0002199!2.80e-07!45;UBERON:0002416!2.80e-07!45;UBERON:0000947!2.99e-07!21;UBERON:0010191!2.99e-07!21;UBERON:0000025!5.18e-07!194;UBERON:0000466!5.45e-07!126
|ontology_enrichment_uberon=UBERON:0003914!2.16e-19!118;UBERON:0002100!1.96e-18!216;UBERON:0005256!5.05e-18!143;UBERON:0000468!2.27e-17!659;UBERON:0004872!8.25e-17!84;UBERON:0000475!2.78e-14!365;UBERON:0000467!4.86e-14!625;UBERON:0000480!7.79e-14!626;UBERON:0000486!1.53e-13!82;UBERON:0003104!2.68e-13!238;UBERON:0009142!2.68e-13!238;UBERON:0000914!2.86e-13!83;UBERON:0002329!2.86e-13!83;UBERON:0003077!2.86e-13!83;UBERON:0003059!2.86e-13!83;UBERON:0007282!2.86e-13!83;UBERON:0009618!2.86e-13!83;UBERON:0007285!2.86e-13!83;UBERON:0000490!4.28e-13!138;UBERON:0001981!6.48e-13!60;UBERON:0007500!6.48e-13!60;UBERON:0004537!6.48e-13!60;UBERON:0006965!6.48e-13!60;UBERON:0004290!6.62e-13!70;UBERON:0000926!7.40e-13!448;UBERON:0004120!7.40e-13!448;UBERON:0006603!7.40e-13!448;UBERON:0002049!1.12e-12!79;UBERON:0007798!1.12e-12!79;UBERON:0001637!1.21e-12!42;UBERON:0003509!1.21e-12!42;UBERON:0004572!1.21e-12!42;UBERON:0000055!2.51e-12!69;UBERON:0000119!4.69e-12!312;UBERON:0000483!6.64e-12!309;UBERON:0001134!1.95e-11!61;UBERON:0002036!1.95e-11!61;UBERON:0003082!1.95e-11!61;UBERON:0002385!2.64e-11!63;UBERON:0001015!2.64e-11!63;UBERON:0000383!2.64e-11!63;UBERON:0001009!3.59e-11!113;UBERON:0004573!6.91e-11!33;UBERON:0004571!6.91e-11!33;UBERON:0004535!7.01e-11!110;UBERON:0000481!2.14e-10!347;UBERON:0000477!6.16e-10!286;UBERON:0000922!8.19e-09!612;UBERON:0002050!9.54e-09!605;UBERON:0005423!9.54e-09!605;UBERON:0000923!9.59e-09!604;UBERON:0005291!9.59e-09!604;UBERON:0006598!9.59e-09!604;UBERON:0002532!9.59e-09!604;UBERON:0001048!1.33e-08!168;UBERON:0004111!1.90e-08!241;UBERON:0004923!6.15e-08!57;UBERON:0003102!1.00e-07!95;UBERON:0009569!2.25e-07!113;UBERON:0001013!2.70e-07!14;UBERON:0002199!2.80e-07!45;UBERON:0002416!2.80e-07!45;UBERON:0000947!2.99e-07!21;UBERON:0010191!2.99e-07!21;UBERON:0000025!5.18e-07!194;UBERON:0000466!5.45e-07!126
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}}
}}

Revision as of 14:23, 5 September 2012


Full id: C2716_Osteoblast_leiomyoma_Preadipocyte_Adipocyte_mesenchymal_Smooth_Mesothelial



Phase1 CAGE Peaks

Hg19::chr3:124606049..124606060,-p9@ITGB5
Hg19::chr3:124606074..124606198,-p1@ITGB5
Hg19::chr3:124606201..124606223,-p2@ITGB5
Hg19::chr3:124606225..124606243,-p6@ITGB5


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
epithelial tube2.16e-19118
trunk1.96e-18216
trunk mesenchyme5.05e-18143
multi-cellular organism2.27e-17659
splanchnic layer of lateral plate mesoderm8.25e-1784
organism subdivision2.78e-14365
anatomical system4.86e-14625
anatomical group7.79e-14626
multilaminar epithelium1.53e-1382
mesenchyme2.68e-13238
entire embryonic mesenchyme2.68e-13238
somite2.86e-1383
paraxial mesoderm2.86e-1383
presomitic mesoderm2.86e-1383
presumptive segmental plate2.86e-1383
trunk paraxial mesoderm2.86e-1383
presumptive paraxial mesoderm2.86e-1383
unilaminar epithelium4.28e-13138
blood vessel6.48e-1360
epithelial tube open at both ends6.48e-1360
blood vasculature6.48e-1360
vascular cord6.48e-1360
dermomyotome6.62e-1370
mesoderm7.40e-13448
mesoderm-derived structure7.40e-13448
presumptive mesoderm7.40e-13448
vasculature1.12e-1279
vascular system1.12e-1279
artery1.21e-1242
arterial blood vessel1.21e-1242
arterial system1.21e-1242
vessel2.51e-1269
cell layer4.69e-12312
epithelium6.64e-12309
skeletal muscle tissue1.95e-1161
striated muscle tissue1.95e-1161
myotome1.95e-1161
muscle tissue2.64e-1163
musculature2.64e-1163
musculature of body2.64e-1163
circulatory system3.59e-11113
systemic artery6.91e-1133
systemic arterial system6.91e-1133
cardiovascular system7.01e-11110
multi-tissue structure2.14e-10347
anatomical cluster6.16e-10286
embryo8.19e-09612
embryonic structure9.54e-09605
developing anatomical structure9.54e-09605
germ layer9.59e-09604
embryonic tissue9.59e-09604
presumptive structure9.59e-09604
epiblast (generic)9.59e-09604
primordium1.33e-08168
anatomical conduit1.90e-08241
organ component layer6.15e-0857
surface structure1.00e-0795
subdivision of trunk2.25e-07113
adipose tissue2.70e-0714
integument2.80e-0745
integumental system2.80e-0745
aorta2.99e-0721
aortic system2.99e-0721
tube5.18e-07194
immaterial anatomical entity5.45e-07126


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#90546.336201576962630.0006203100587215640.00513063769880585
E2F1#186944.907389214879320.001724022357361790.010665511845783
EGR1#195844.988179094810140.001615011500076050.0101577950049047
ETS1#211349.728760922202340.0001115955317418140.00154718249563033
HEY1#2346244.040111043105710.00375304636917980.018641004886611
HMGN3#932448.178547723350590.0002234570284440470.00248457666279866
MYC#460945.22228187160940.001344309395272740.0088865326243996
SMARCB1#6598418.25271578115749.00423392720929e-060.000241995158806951
TAF1#687243.343046285745290.008005664898701650.0322832401388278
TAF7#6879411.43306940492395.85061525419808e-050.00097081729668445
TBP#690843.706770687096390.005296377814784350.024469096814928
ZNF263#1012748.221841637010680.0002187871180958320.00249453142214089



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.