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Coexpression cluster:C3710: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000025!3.77e-23!194;UBERON:0003914!2.19e-22!118;UBERON:0000119!2.52e-19!312;UBERON:0000483!3.03e-19!309;UBERON:0000475!3.62e-19!365;UBERON:0000477!2.98e-18!286;UBERON:0004872!7.44e-18!84;UBERON:0001009!2.17e-17!113;UBERON:0004111!1.11e-16!241;UBERON:0004535!3.94e-16!110;UBERON:0001637!1.30e-15!42;UBERON:0003509!1.30e-15!42;UBERON:0004572!1.30e-15!42;UBERON:0000481!5.33e-15!347;UBERON:0000468!1.22e-14!659;UBERON:0002049!1.88e-14!79;UBERON:0007798!1.88e-14!79;UBERON:0005256!5.02e-14!143;UBERON:0001981!8.73e-14!60;UBERON:0007500!8.73e-14!60;UBERON:0004537!8.73e-14!60;UBERON:0006965!8.73e-14!60;UBERON:0001134!7.20e-13!61;UBERON:0002036!7.20e-13!61;UBERON:0003082!7.20e-13!61;UBERON:0004573!1.22e-12!33;UBERON:0004571!1.22e-12!33;UBERON:0000055!2.40e-12!69;UBERON:0000467!3.90e-12!625;UBERON:0002385!3.95e-12!63;UBERON:0001015!3.95e-12!63;UBERON:0000383!3.95e-12!63;UBERON:0007100!6.06e-12!27;UBERON:0000480!7.15e-12!626;UBERON:0000914!2.64e-11!83;UBERON:0002329!2.64e-11!83;UBERON:0003077!2.64e-11!83;UBERON:0003059!2.64e-11!83;UBERON:0007282!2.64e-11!83;UBERON:0009618!2.64e-11!83;UBERON:0007285!2.64e-11!83;UBERON:0004290!5.32e-11!70;UBERON:0002100!1.31e-10!216;UBERON:0000490!1.33e-10!138;UBERON:0000948!1.76e-10!24;UBERON:0005498!1.76e-10!24;UBERON:0004140!1.76e-10!24;UBERON:0009881!1.76e-10!24;UBERON:0004141!1.76e-10!24;UBERON:0003084!1.76e-10!24;UBERON:0007005!1.76e-10!24;UBERON:0004139!1.76e-10!24;UBERON:0004291!1.76e-10!24;UBERON:0000073!2.61e-09!94;UBERON:0001016!2.61e-09!94;UBERON:0000486!3.15e-09!82;UBERON:0005743!5.98e-09!86;UBERON:0000922!9.10e-09!612;UBERON:0001017!3.98e-08!82;UBERON:0002050!4.05e-08!605;UBERON:0005423!4.05e-08!605;UBERON:0003103!4.49e-08!69;UBERON:0000923!4.51e-08!604;UBERON:0005291!4.51e-08!604;UBERON:0006598!4.51e-08!604;UBERON:0002532!4.51e-08!604;UBERON:0003075!9.11e-08!86;UBERON:0007284!9.11e-08!86;UBERON:0000947!7.97e-07!21;UBERON:0010191!7.97e-07!21
|ontology_enrichment_uberon=UBERON:0000025!3.77e-23!194;UBERON:0003914!2.19e-22!118;UBERON:0000119!2.52e-19!312;UBERON:0000483!3.03e-19!309;UBERON:0000475!3.62e-19!365;UBERON:0000477!2.98e-18!286;UBERON:0004872!7.44e-18!84;UBERON:0001009!2.17e-17!113;UBERON:0004111!1.11e-16!241;UBERON:0004535!3.94e-16!110;UBERON:0001637!1.30e-15!42;UBERON:0003509!1.30e-15!42;UBERON:0004572!1.30e-15!42;UBERON:0000481!5.33e-15!347;UBERON:0000468!1.22e-14!659;UBERON:0002049!1.88e-14!79;UBERON:0007798!1.88e-14!79;UBERON:0005256!5.02e-14!143;UBERON:0001981!8.73e-14!60;UBERON:0007500!8.73e-14!60;UBERON:0004537!8.73e-14!60;UBERON:0006965!8.73e-14!60;UBERON:0001134!7.20e-13!61;UBERON:0002036!7.20e-13!61;UBERON:0003082!7.20e-13!61;UBERON:0004573!1.22e-12!33;UBERON:0004571!1.22e-12!33;UBERON:0000055!2.40e-12!69;UBERON:0000467!3.90e-12!625;UBERON:0002385!3.95e-12!63;UBERON:0001015!3.95e-12!63;UBERON:0000383!3.95e-12!63;UBERON:0007100!6.06e-12!27;UBERON:0000480!7.15e-12!626;UBERON:0000914!2.64e-11!83;UBERON:0002329!2.64e-11!83;UBERON:0003077!2.64e-11!83;UBERON:0003059!2.64e-11!83;UBERON:0007282!2.64e-11!83;UBERON:0009618!2.64e-11!83;UBERON:0007285!2.64e-11!83;UBERON:0004290!5.32e-11!70;UBERON:0002100!1.31e-10!216;UBERON:0000490!1.33e-10!138;UBERON:0000948!1.76e-10!24;UBERON:0005498!1.76e-10!24;UBERON:0004140!1.76e-10!24;UBERON:0009881!1.76e-10!24;UBERON:0004141!1.76e-10!24;UBERON:0003084!1.76e-10!24;UBERON:0007005!1.76e-10!24;UBERON:0004139!1.76e-10!24;UBERON:0004291!1.76e-10!24;UBERON:0000073!2.61e-09!94;UBERON:0001016!2.61e-09!94;UBERON:0000486!3.15e-09!82;UBERON:0005743!5.98e-09!86;UBERON:0000922!9.10e-09!612;UBERON:0001017!3.98e-08!82;UBERON:0002050!4.05e-08!605;UBERON:0005423!4.05e-08!605;UBERON:0003103!4.49e-08!69;UBERON:0000923!4.51e-08!604;UBERON:0005291!4.51e-08!604;UBERON:0006598!4.51e-08!604;UBERON:0002532!4.51e-08!604;UBERON:0003075!9.11e-08!86;UBERON:0007284!9.11e-08!86;UBERON:0000947!7.97e-07!21;UBERON:0010191!7.97e-07!21
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}}
}}

Revision as of 12:13, 5 September 2012


Full id: C3710_Smooth_Fibroblast_heart_Neural_Preadipocyte_cholangiocellular_Lens



Phase1 CAGE Peaks

Hg19::chr18:25756974..25757018,-p2@CDH2
Hg19::chr18:25757019..25757024,-p6@CDH2
Hg19::chr18:25757066..25757103,-p1@CDH2


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
tube3.77e-23194
epithelial tube2.19e-22118
cell layer2.52e-19312
epithelium3.03e-19309
organism subdivision3.62e-19365
anatomical cluster2.98e-18286
splanchnic layer of lateral plate mesoderm7.44e-1884
circulatory system2.17e-17113
anatomical conduit1.11e-16241
cardiovascular system3.94e-16110
artery1.30e-1542
arterial blood vessel1.30e-1542
arterial system1.30e-1542
multi-tissue structure5.33e-15347
multi-cellular organism1.22e-14659
vasculature1.88e-1479
vascular system1.88e-1479
trunk mesenchyme5.02e-14143
blood vessel8.73e-1460
epithelial tube open at both ends8.73e-1460
blood vasculature8.73e-1460
vascular cord8.73e-1460
skeletal muscle tissue7.20e-1361
striated muscle tissue7.20e-1361
myotome7.20e-1361
systemic artery1.22e-1233
systemic arterial system1.22e-1233
vessel2.40e-1269
anatomical system3.90e-12625
muscle tissue3.95e-1263
musculature3.95e-1263
musculature of body3.95e-1263
primary circulatory organ6.06e-1227
anatomical group7.15e-12626
somite2.64e-1183
paraxial mesoderm2.64e-1183
presomitic mesoderm2.64e-1183
presumptive segmental plate2.64e-1183
trunk paraxial mesoderm2.64e-1183
presumptive paraxial mesoderm2.64e-1183
dermomyotome5.32e-1170
trunk1.31e-10216
unilaminar epithelium1.33e-10138
heart1.76e-1024
primitive heart tube1.76e-1024
primary heart field1.76e-1024
anterior lateral plate mesoderm1.76e-1024
heart tube1.76e-1024
heart primordium1.76e-1024
cardiac mesoderm1.76e-1024
cardiogenic plate1.76e-1024
heart rudiment1.76e-1024
regional part of nervous system2.61e-0994
nervous system2.61e-0994
multilaminar epithelium3.15e-0982
embryo9.10e-09612
central nervous system3.98e-0882
embryonic structure4.05e-08605
developing anatomical structure4.05e-08605
compound organ4.49e-0869
germ layer4.51e-08604
embryonic tissue4.51e-08604
presumptive structure4.51e-08604
epiblast (generic)4.51e-08604
neural plate9.11e-0886
presumptive neural plate9.11e-0886
aorta7.97e-0721
aortic system7.97e-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
EP300#203336.77394172622320.003216880500103790.0167389657989308
HDAC2#3066313.41562023662630.0004140761399857210.00391116016857816
RAD21#5885310.35503389545630.0009004912073565420.00663747626544639



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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