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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C506_Smooth_Renal_Endothelial_hepatic_Adipocyte_Fibroblast_Preadipocyte
|full_id=C506_Smooth_Renal_Endothelial_hepatic_Adipocyte_Fibroblast_Preadipocyte
|id=C506
|id=C506

Revision as of 18:04, 12 September 2012


Full id: C506_Smooth_Renal_Endothelial_hepatic_Adipocyte_Fibroblast_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr6:132269835..132269894,-p7@CTGF
Hg19::chr6:132269939..132269966,-p12@CTGF
Hg19::chr6:132270118..132270130,-p13@CTGF
Hg19::chr6:132270276..132270290,-p10@CTGF
Hg19::chr6:132270471..132270530,-p5@CTGF
Hg19::chr6:132270532..132270550,-p9@CTGF
Hg19::chr6:132270563..132270604,-p3@CTGF
Hg19::chr6:132270672..132270706,-p8@CTGF
Hg19::chr6:132271115..132271160,-p@chr6:132271115..132271160
-
Hg19::chr6:132271128..132271174,+p@chr6:132271128..132271174
+
Hg19::chr6:132271161..132271207,-p@chr6:132271161..132271207
-
Hg19::chr6:132271279..132271304,-p@chr6:132271279..132271304
-
Hg19::chr6:132271546..132271561,-p@chr6:132271546..132271561
-
Hg19::chr6:132271569..132271590,-p@chr6:132271569..132271590
-
Hg19::chr6:132271627..132271658,-p@chr6:132271627..132271658
-
Hg19::chr6:132271932..132271967,-p6@CTGF
Hg19::chr6:132271980..132271991,-p16@CTGF
Hg19::chr6:132271998..132272086,-p2@CTGF
Hg19::chr6:132272504..132272519,-p1@CTGF


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
vasculature3.83e-3079
vascular system3.83e-3079
epithelial tube4.61e-29118
splanchnic layer of lateral plate mesoderm2.46e-2784
vessel6.44e-2669
blood vessel8.01e-2460
epithelial tube open at both ends8.01e-2460
blood vasculature8.01e-2460
vascular cord8.01e-2460
unilaminar epithelium1.08e-21138
cardiovascular system1.23e-21110
circulatory system2.57e-21113
anatomical cluster2.00e-20286
cell layer2.50e-20312
trunk mesenchyme2.60e-20143
epithelium9.15e-20309
trunk2.60e-19216
artery3.80e-1942
arterial blood vessel3.80e-1942
arterial system3.80e-1942
organism subdivision7.72e-19365
multi-cellular organism2.18e-18659
anatomical conduit7.28e-17241
multi-tissue structure5.25e-16347
somite1.41e-1583
paraxial mesoderm1.41e-1583
presomitic mesoderm1.41e-1583
presumptive segmental plate1.41e-1583
trunk paraxial mesoderm1.41e-1583
presumptive paraxial mesoderm1.41e-1583
muscle tissue4.71e-1563
musculature4.71e-1563
musculature of body4.71e-1563
skeletal muscle tissue6.17e-1561
striated muscle tissue6.17e-1561
myotome6.17e-1561
systemic artery6.83e-1533
systemic arterial system6.83e-1533
anatomical system1.91e-14625
mesenchyme2.12e-14238
entire embryonic mesenchyme2.12e-14238
dermomyotome2.76e-1470
anatomical group4.03e-14626
tube6.42e-14194
multilaminar epithelium1.11e-1382
aorta2.73e-1021
aortic system2.73e-1021
squamous epithelium9.21e-1025
simple squamous epithelium1.64e-0922
embryo3.29e-09612
embryonic structure5.78e-09605
developing anatomical structure5.78e-09605
germ layer8.46e-09604
embryonic tissue8.46e-09604
presumptive structure8.46e-09604
epiblast (generic)8.46e-09604
endothelium1.12e-0818
blood vessel endothelium1.12e-0818
cardiovascular system endothelium1.12e-0818
mesoderm1.60e-08448
mesoderm-derived structure1.60e-08448
presumptive mesoderm1.60e-08448
subdivision of trunk2.19e-08113
compound organ1.33e-0769
heart1.52e-0724
primitive heart tube1.52e-0724
primary heart field1.52e-0724
anterior lateral plate mesoderm1.52e-0724
heart tube1.52e-0724
heart primordium1.52e-0724
cardiac mesoderm1.52e-0724
cardiogenic plate1.52e-0724
heart rudiment1.52e-0724
primary circulatory organ4.86e-0727
primordium6.79e-07168


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#10664123.38542507773162.39602138640007e-050.000522308657011557
GATA3#262568.601005165433484.38557728836884e-050.000777764147427328
HEY1#23462194.040111043105713.00127317794054e-123.98791309708564e-10
JUN#372574.60998970243970.0004418850707130040.00411612869248978
JUND#3727165.890243319470341.90674971775736e-112.29422849968734e-09
NR3C1#290875.516377016747960.000145422501243130.00187967581773901
POLR2A#5430192.147453176558074.9316078952508e-072.31380142395372e-05
POU5F1#5460352.96408443977462.46415883246597e-050.00053404084727934
RAD21#5885105.450017839713862.85321341547804e-069.81511053686135e-05
STAT3#677463.321936314890810.006719751575040510.0285622943610621
TAF7#68791810.83132890992791.55076047024434e-183.52853753272002e-16
USF2#739274.786599036604590.0003509309921958220.00353261512230742



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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