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Coexpression cluster:C2059: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!5.86e-19!659;UBERON:0005256!1.20e-18!143;UBERON:0002100!9.68e-18!216;UBERON:0000914!2.71e-17!83;UBERON:0002329!2.71e-17!83;UBERON:0003077!2.71e-17!83;UBERON:0003059!2.71e-17!83;UBERON:0007282!2.71e-17!83;UBERON:0009618!2.71e-17!83;UBERON:0007285!2.71e-17!83;UBERON:0000475!7.66e-16!365;UBERON:0004290!7.78e-16!70;UBERON:0000467!3.83e-15!625;UBERON:0000480!8.63e-15!626;UBERON:0000486!1.19e-14!82;UBERON:0003914!2.06e-14!118;UBERON:0001134!9.81e-14!61;UBERON:0002036!9.81e-14!61;UBERON:0003082!9.81e-14!61;UBERON:0002049!1.57e-13!79;UBERON:0007798!1.57e-13!79;UBERON:0002385!2.53e-13!63;UBERON:0001015!2.53e-13!63;UBERON:0000383!2.53e-13!63;UBERON:0000490!9.59e-13!138;UBERON:0004872!1.75e-12!84;UBERON:0003104!2.92e-12!238;UBERON:0009142!2.92e-12!238;UBERON:0000481!9.78e-12!347;UBERON:0000119!2.09e-11!312;UBERON:0000055!5.09e-11!69;UBERON:0000483!5.28e-11!309;UBERON:0003102!8.98e-11!95;UBERON:0001981!2.31e-10!60;UBERON:0007500!2.31e-10!60;UBERON:0004537!2.31e-10!60;UBERON:0006965!2.31e-10!60;UBERON:0001009!3.79e-10!113;UBERON:0004535!7.09e-10!110;UBERON:0002050!7.11e-10!605;UBERON:0005423!7.11e-10!605;UBERON:0000922!7.11e-10!612;UBERON:0001637!9.41e-10!42;UBERON:0003509!9.41e-10!42;UBERON:0004572!9.41e-10!42;UBERON:0000926!1.39e-09!448;UBERON:0004120!1.39e-09!448;UBERON:0006603!1.39e-09!448;UBERON:0000923!1.47e-09!604;UBERON:0005291!1.47e-09!604;UBERON:0006598!1.47e-09!604;UBERON:0002532!1.47e-09!604;UBERON:0004573!2.06e-09!33;UBERON:0004571!2.06e-09!33;UBERON:0000477!4.80e-09!286;UBERON:0002199!9.66e-09!45;UBERON:0002416!9.66e-09!45;UBERON:0002097!1.95e-08!40;UBERON:0004111!1.30e-07!241;UBERON:0000947!2.48e-07!21;UBERON:0010191!2.48e-07!21
|ontology_enrichment_uberon=UBERON:0000468!5.86e-19!659;UBERON:0005256!1.20e-18!143;UBERON:0002100!9.68e-18!216;UBERON:0000914!2.71e-17!83;UBERON:0002329!2.71e-17!83;UBERON:0003077!2.71e-17!83;UBERON:0003059!2.71e-17!83;UBERON:0007282!2.71e-17!83;UBERON:0009618!2.71e-17!83;UBERON:0007285!2.71e-17!83;UBERON:0000475!7.66e-16!365;UBERON:0004290!7.78e-16!70;UBERON:0000467!3.83e-15!625;UBERON:0000480!8.63e-15!626;UBERON:0000486!1.19e-14!82;UBERON:0003914!2.06e-14!118;UBERON:0001134!9.81e-14!61;UBERON:0002036!9.81e-14!61;UBERON:0003082!9.81e-14!61;UBERON:0002049!1.57e-13!79;UBERON:0007798!1.57e-13!79;UBERON:0002385!2.53e-13!63;UBERON:0001015!2.53e-13!63;UBERON:0000383!2.53e-13!63;UBERON:0000490!9.59e-13!138;UBERON:0004872!1.75e-12!84;UBERON:0003104!2.92e-12!238;UBERON:0009142!2.92e-12!238;UBERON:0000481!9.78e-12!347;UBERON:0000119!2.09e-11!312;UBERON:0000055!5.09e-11!69;UBERON:0000483!5.28e-11!309;UBERON:0003102!8.98e-11!95;UBERON:0001981!2.31e-10!60;UBERON:0007500!2.31e-10!60;UBERON:0004537!2.31e-10!60;UBERON:0006965!2.31e-10!60;UBERON:0001009!3.79e-10!113;UBERON:0004535!7.09e-10!110;UBERON:0002050!7.11e-10!605;UBERON:0005423!7.11e-10!605;UBERON:0000922!7.11e-10!612;UBERON:0001637!9.41e-10!42;UBERON:0003509!9.41e-10!42;UBERON:0004572!9.41e-10!42;UBERON:0000926!1.39e-09!448;UBERON:0004120!1.39e-09!448;UBERON:0006603!1.39e-09!448;UBERON:0000923!1.47e-09!604;UBERON:0005291!1.47e-09!604;UBERON:0006598!1.47e-09!604;UBERON:0002532!1.47e-09!604;UBERON:0004573!2.06e-09!33;UBERON:0004571!2.06e-09!33;UBERON:0000477!4.80e-09!286;UBERON:0002199!9.66e-09!45;UBERON:0002416!9.66e-09!45;UBERON:0002097!1.95e-08!40;UBERON:0004111!1.30e-07!241;UBERON:0000947!2.48e-07!21;UBERON:0010191!2.48e-07!21
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00815280776754614!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433348824966487!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172598885858973!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195677598024727!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248018102972002
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}}
}}

Revision as of 13:36, 5 September 2012


Full id: C2059_Myoblast_prostate_tridermal_mucinous_myxofibrosarcoma_mesenchymal_osteosarcoma



Phase1 CAGE Peaks

Hg19::chr10:33623685..33623700,-p7@NRP1
Hg19::chr10:33623764..33623777,-p6@NRP1
Hg19::chr10:33623784..33623806,-p1@NRP1
Hg19::chr10:33623826..33623835,-p9@NRP1


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
multi-cellular organism5.86e-19659
trunk mesenchyme1.20e-18143
trunk9.68e-18216
somite2.71e-1783
paraxial mesoderm2.71e-1783
presomitic mesoderm2.71e-1783
presumptive segmental plate2.71e-1783
trunk paraxial mesoderm2.71e-1783
presumptive paraxial mesoderm2.71e-1783
organism subdivision7.66e-16365
dermomyotome7.78e-1670
anatomical system3.83e-15625
anatomical group8.63e-15626
multilaminar epithelium1.19e-1482
epithelial tube2.06e-14118
skeletal muscle tissue9.81e-1461
striated muscle tissue9.81e-1461
myotome9.81e-1461
vasculature1.57e-1379
vascular system1.57e-1379
muscle tissue2.53e-1363
musculature2.53e-1363
musculature of body2.53e-1363
unilaminar epithelium9.59e-13138
splanchnic layer of lateral plate mesoderm1.75e-1284
mesenchyme2.92e-12238
entire embryonic mesenchyme2.92e-12238
multi-tissue structure9.78e-12347
cell layer2.09e-11312
vessel5.09e-1169
epithelium5.28e-11309
surface structure8.98e-1195
blood vessel2.31e-1060
epithelial tube open at both ends2.31e-1060
blood vasculature2.31e-1060
vascular cord2.31e-1060
circulatory system3.79e-10113
cardiovascular system7.09e-10110
embryonic structure7.11e-10605
developing anatomical structure7.11e-10605
embryo7.11e-10612
artery9.41e-1042
arterial blood vessel9.41e-1042
arterial system9.41e-1042
mesoderm1.39e-09448
mesoderm-derived structure1.39e-09448
presumptive mesoderm1.39e-09448
germ layer1.47e-09604
embryonic tissue1.47e-09604
presumptive structure1.47e-09604
epiblast (generic)1.47e-09604
systemic artery2.06e-0933
systemic arterial system2.06e-0933
anatomical cluster4.80e-09286
integument9.66e-0945
integumental system9.66e-0945
skin of body1.95e-0840
anatomical conduit1.30e-07241
aorta2.48e-0721
aortic system2.48e-0721


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#1066445.360256373075030.001211145381643620.00815280776754614
EP300#203346.77394172622320.0004748459821442640.00433348824966487
RAD21#588537.766275421592250.0033411193858720.0172598885858973
REST#597837.237521537096020.004104697304192610.0195677598024727
ZNF263#1012748.221841637010680.0002187871180958320.00248018102972002



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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