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Coexpression cluster:C3498: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000055!1.30e-28!69;UBERON:0004872!1.23e-27!84;UBERON:0002049!5.03e-27!79;UBERON:0007798!5.03e-27!79;UBERON:0001981!4.08e-25!60;UBERON:0007500!4.08e-25!60;UBERON:0004537!4.08e-25!60;UBERON:0006965!4.08e-25!60;UBERON:0001009!1.96e-22!113;UBERON:0004535!5.73e-22!110;UBERON:0004111!1.18e-21!241;UBERON:0000119!5.09e-20!312;UBERON:0000483!1.76e-19!309;UBERON:0003914!1.87e-19!118;UBERON:0000477!1.94e-19!286;UBERON:0000025!2.45e-19!194;UBERON:0000468!1.11e-18!659;UBERON:0004290!2.89e-18!70;UBERON:0001637!3.71e-18!42;UBERON:0003509!3.71e-18!42;UBERON:0004572!3.71e-18!42;UBERON:0000467!7.61e-18!625;UBERON:0002385!1.46e-17!63;UBERON:0001015!1.46e-17!63;UBERON:0000383!1.46e-17!63;UBERON:0000480!1.53e-17!626;UBERON:0001134!4.47e-17!61;UBERON:0002036!4.47e-17!61;UBERON:0003082!4.47e-17!61;UBERON:0000914!6.71e-17!83;UBERON:0002329!6.71e-17!83;UBERON:0003077!6.71e-17!83;UBERON:0003059!6.71e-17!83;UBERON:0007282!6.71e-17!83;UBERON:0009618!6.71e-17!83;UBERON:0007285!6.71e-17!83;UBERON:0000490!9.28e-16!138;UBERON:0000486!2.55e-14!82;UBERON:0004573!7.85e-14!33;UBERON:0004571!7.85e-14!33;UBERON:0005256!1.22e-12!143;UBERON:0001986!1.27e-12!18;UBERON:0004638!1.27e-12!18;UBERON:0004852!1.27e-12!18;UBERON:0002050!3.95e-12!605;UBERON:0005423!3.95e-12!605;UBERON:0000923!7.99e-12!604;UBERON:0005291!7.99e-12!604;UBERON:0006598!7.99e-12!604;UBERON:0002532!7.99e-12!604;UBERON:0000922!9.43e-12!612;UBERON:0000475!2.44e-11!365;UBERON:0007023!5.04e-11!115;UBERON:0000947!2.04e-10!21;UBERON:0010191!2.04e-10!21;UBERON:0000487!6.10e-10!22;UBERON:0000926!7.38e-10!448;UBERON:0004120!7.38e-10!448;UBERON:0006603!7.38e-10!448;UBERON:0006914!1.83e-09!25;UBERON:0002100!6.02e-09!216;UBERON:0000481!6.16e-09!347;UBERON:0007100!1.41e-08!27;UBERON:0000948!2.88e-08!24;UBERON:0005498!2.88e-08!24;UBERON:0004140!2.88e-08!24;UBERON:0009881!2.88e-08!24;UBERON:0004141!2.88e-08!24;UBERON:0003084!2.88e-08!24;UBERON:0007005!2.88e-08!24;UBERON:0004139!2.88e-08!24;UBERON:0004291!2.88e-08!24;UBERON:0003915!6.52e-07!9;UBERON:0004700!6.52e-07!9;UBERON:0001917!6.52e-07!9
|ontology_enrichment_uberon=UBERON:0000055!1.30e-28!69;UBERON:0004872!1.23e-27!84;UBERON:0002049!5.03e-27!79;UBERON:0007798!5.03e-27!79;UBERON:0001981!4.08e-25!60;UBERON:0007500!4.08e-25!60;UBERON:0004537!4.08e-25!60;UBERON:0006965!4.08e-25!60;UBERON:0001009!1.96e-22!113;UBERON:0004535!5.73e-22!110;UBERON:0004111!1.18e-21!241;UBERON:0000119!5.09e-20!312;UBERON:0000483!1.76e-19!309;UBERON:0003914!1.87e-19!118;UBERON:0000477!1.94e-19!286;UBERON:0000025!2.45e-19!194;UBERON:0000468!1.11e-18!659;UBERON:0004290!2.89e-18!70;UBERON:0001637!3.71e-18!42;UBERON:0003509!3.71e-18!42;UBERON:0004572!3.71e-18!42;UBERON:0000467!7.61e-18!625;UBERON:0002385!1.46e-17!63;UBERON:0001015!1.46e-17!63;UBERON:0000383!1.46e-17!63;UBERON:0000480!1.53e-17!626;UBERON:0001134!4.47e-17!61;UBERON:0002036!4.47e-17!61;UBERON:0003082!4.47e-17!61;UBERON:0000914!6.71e-17!83;UBERON:0002329!6.71e-17!83;UBERON:0003077!6.71e-17!83;UBERON:0003059!6.71e-17!83;UBERON:0007282!6.71e-17!83;UBERON:0009618!6.71e-17!83;UBERON:0007285!6.71e-17!83;UBERON:0000490!9.28e-16!138;UBERON:0000486!2.55e-14!82;UBERON:0004573!7.85e-14!33;UBERON:0004571!7.85e-14!33;UBERON:0005256!1.22e-12!143;UBERON:0001986!1.27e-12!18;UBERON:0004638!1.27e-12!18;UBERON:0004852!1.27e-12!18;UBERON:0002050!3.95e-12!605;UBERON:0005423!3.95e-12!605;UBERON:0000923!7.99e-12!604;UBERON:0005291!7.99e-12!604;UBERON:0006598!7.99e-12!604;UBERON:0002532!7.99e-12!604;UBERON:0000922!9.43e-12!612;UBERON:0000475!2.44e-11!365;UBERON:0007023!5.04e-11!115;UBERON:0000947!2.04e-10!21;UBERON:0010191!2.04e-10!21;UBERON:0000487!6.10e-10!22;UBERON:0000926!7.38e-10!448;UBERON:0004120!7.38e-10!448;UBERON:0006603!7.38e-10!448;UBERON:0006914!1.83e-09!25;UBERON:0002100!6.02e-09!216;UBERON:0000481!6.16e-09!347;UBERON:0007100!1.41e-08!27;UBERON:0000948!2.88e-08!24;UBERON:0005498!2.88e-08!24;UBERON:0004140!2.88e-08!24;UBERON:0009881!2.88e-08!24;UBERON:0004141!2.88e-08!24;UBERON:0003084!2.88e-08!24;UBERON:0007005!2.88e-08!24;UBERON:0004139!2.88e-08!24;UBERON:0004291!2.88e-08!24;UBERON:0003915!6.52e-07!9;UBERON:0004700!6.52e-07!9;UBERON:0001917!6.52e-07!9
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}}
}}

Revision as of 12:47, 5 September 2012


Full id: C3498_Myoblast_Mesothelial_Endothelial_myxofibrosarcoma_mesenchymal_Lymphatic_immature



Phase1 CAGE Peaks

Hg19::chr15:51386859..51386938,-p3@TNFAIP8L3
Hg19::chr15:51386999..51387039,-p1@TNFAIP8L3
Hg19::chr15:51387094..51387110,-p2@TNFAIP8L3


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
vessel1.30e-2869
splanchnic layer of lateral plate mesoderm1.23e-2784
vasculature5.03e-2779
vascular system5.03e-2779
blood vessel4.08e-2560
epithelial tube open at both ends4.08e-2560
blood vasculature4.08e-2560
vascular cord4.08e-2560
circulatory system1.96e-22113
cardiovascular system5.73e-22110
anatomical conduit1.18e-21241
cell layer5.09e-20312
epithelium1.76e-19309
epithelial tube1.87e-19118
anatomical cluster1.94e-19286
tube2.45e-19194
multi-cellular organism1.11e-18659
dermomyotome2.89e-1870
artery3.71e-1842
arterial blood vessel3.71e-1842
arterial system3.71e-1842
anatomical system7.61e-18625
muscle tissue1.46e-1763
musculature1.46e-1763
musculature of body1.46e-1763
anatomical group1.53e-17626
skeletal muscle tissue4.47e-1761
striated muscle tissue4.47e-1761
myotome4.47e-1761
somite6.71e-1783
paraxial mesoderm6.71e-1783
presomitic mesoderm6.71e-1783
presumptive segmental plate6.71e-1783
trunk paraxial mesoderm6.71e-1783
presumptive paraxial mesoderm6.71e-1783
unilaminar epithelium9.28e-16138
multilaminar epithelium2.55e-1482
systemic artery7.85e-1433
systemic arterial system7.85e-1433
trunk mesenchyme1.22e-12143
endothelium1.27e-1218
blood vessel endothelium1.27e-1218
cardiovascular system endothelium1.27e-1218
embryonic structure3.95e-12605
developing anatomical structure3.95e-12605
germ layer7.99e-12604
embryonic tissue7.99e-12604
presumptive structure7.99e-12604
epiblast (generic)7.99e-12604
embryo9.43e-12612
organism subdivision2.44e-11365
adult organism5.04e-11115
aorta2.04e-1021
aortic system2.04e-1021
simple squamous epithelium6.10e-1022
mesoderm7.38e-10448
mesoderm-derived structure7.38e-10448
presumptive mesoderm7.38e-10448
squamous epithelium1.83e-0925
trunk6.02e-09216
multi-tissue structure6.16e-09347
primary circulatory organ1.41e-0827
heart2.88e-0824
primitive heart tube2.88e-0824
primary heart field2.88e-0824
anterior lateral plate mesoderm2.88e-0824
heart tube2.88e-0824
heart primordium2.88e-0824
cardiac mesoderm2.88e-0824
cardiogenic plate2.88e-0824
heart rudiment2.88e-0824
endothelial tube6.52e-079
arterial system endothelium6.52e-079
endothelium of artery6.52e-079


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
E2F1#186934.907389214879320.008460985347239390.0324551676159817
ZNF263#1012738.221841637010680.001799043925565870.0109175100837986



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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