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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C454_Placental_Amniotic_Smooth_Mesenchymal_Lens_Renal_bile
|full_id=C454_Placental_Amniotic_Smooth_Mesenchymal_Lens_Renal_bile
|id=C454
|id=C454

Revision as of 17:38, 12 September 2012


Full id: C454_Placental_Amniotic_Smooth_Mesenchymal_Lens_Renal_bile



Phase1 CAGE Peaks

Hg19::chr20:36757631..36757652,-p@chr20:36757631..36757652
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Hg19::chr20:36757658..36757727,-p@chr20:36757658..36757727
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Hg19::chr20:36758336..36758366,-p5@TGM2
Hg19::chr20:36758421..36758453,-p9@TGM2
Hg19::chr20:36758577..36758603,-p16@TGM2
Hg19::chr20:36758636..36758676,-p10@TGM2
Hg19::chr20:36766606..36766630,-p7@TGM2
Hg19::chr20:36766683..36766700,-p14@TGM2
Hg19::chr20:36766747..36766778,-p3@TGM2
Hg19::chr20:36767838..36767854,-p@chr20:36767838..36767854
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Hg19::chr20:36767860..36767871,-p@chr20:36767860..36767871
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Hg19::chr20:36767877..36767891,-p@chr20:36767877..36767891
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Hg19::chr20:36767914..36767938,-p@chr20:36767914..36767938
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Hg19::chr20:36768004..36768016,-p@chr20:36768004..36768016
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Hg19::chr20:36768047..36768061,-p@chr20:36768047..36768061
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Hg19::chr20:36770579..36770603,-p@chr20:36770579..36770603
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Hg19::chr20:36776392..36776431,-p@chr20:36776392..36776431
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Hg19::chr20:36779386..36779404,-p@chr20:36779386..36779404
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Hg19::chr20:36784334..36784364,-p@chr20:36784334..36784364
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Hg19::chr20:36784443..36784469,-p@chr20:36784443..36784469
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Hg19::chr20:36793649..36793659,-p2@TGM2
Hg19::chr20:36793663..36793735,-p1@TGM2


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 tube6.24e-33118
vasculature4.32e-2979
vascular system4.32e-2979
anatomical cluster6.12e-27286
multi-cellular organism1.09e-25659
vessel2.02e-2569
splanchnic layer of lateral plate mesoderm6.40e-2584
cell layer2.85e-24312
anatomical conduit4.23e-24241
epithelium1.42e-23309
blood vessel2.04e-2360
epithelial tube open at both ends2.04e-2360
blood vasculature2.04e-2360
vascular cord2.04e-2360
circulatory system4.28e-23113
anatomical system1.21e-22625
anatomical group3.35e-22626
unilaminar epithelium4.94e-22138
cardiovascular system1.06e-21110
trunk mesenchyme2.17e-21143
multi-tissue structure1.56e-20347
tube1.84e-20194
trunk1.60e-19216
embryonic structure7.85e-18605
developing anatomical structure7.85e-18605
germ layer1.75e-17604
embryonic tissue1.75e-17604
presumptive structure1.75e-17604
epiblast (generic)1.75e-17604
mesoderm2.35e-17448
mesoderm-derived structure2.35e-17448
presumptive mesoderm2.35e-17448
embryo8.46e-17612
artery1.51e-1642
arterial blood vessel1.51e-1642
arterial system1.51e-1642
mesenchyme2.14e-16238
entire embryonic mesenchyme2.14e-16238
organism subdivision3.29e-13365
systemic artery5.39e-1333
systemic arterial system5.39e-1333
muscle tissue4.67e-1163
musculature4.67e-1163
musculature of body4.67e-1163
somite7.77e-1183
paraxial mesoderm7.77e-1183
presomitic mesoderm7.77e-1183
presumptive segmental plate7.77e-1183
trunk paraxial mesoderm7.77e-1183
presumptive paraxial mesoderm7.77e-1183
multilaminar epithelium8.51e-1182
skeletal muscle tissue1.09e-1061
striated muscle tissue1.09e-1061
myotome1.09e-1061
dermomyotome3.58e-1070
compound organ5.58e-1069
lateral plate mesoderm1.63e-09216
organ3.73e-09511
endothelium7.49e-0918
blood vessel endothelium7.49e-0918
cardiovascular system endothelium7.49e-0918
extraembryonic membrane7.90e-0914
membranous layer7.90e-0914
simple squamous epithelium9.55e-0922
intermediate mesoderm9.70e-0937
organ part1.05e-08219
renal system1.54e-0845
aorta1.82e-0821
aortic system1.82e-0821
urinary system structure1.83e-0844
tissue3.91e-08787
subdivision of trunk7.14e-08113
squamous epithelium1.42e-0725
parenchyma1.55e-0717
endoderm-derived structure1.56e-07169
endoderm1.56e-07169


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
GATA2#262463.475890472787450.005791119096792690.026038345417166
GATA3#262544.952093883128370.007815040484215180.0321020654132134



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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