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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C758_Chondrocyte_Amniotic_Smooth_Fibroblast_Pericytes_Endothelial_Urothelial
|full_id=C758_Chondrocyte_Amniotic_Smooth_Fibroblast_Pericytes_Endothelial_Urothelial
|id=C758
|id=C758

Revision as of 18:28, 12 September 2012


Full id: C758_Chondrocyte_Amniotic_Smooth_Fibroblast_Pericytes_Endothelial_Urothelial



Phase1 CAGE Peaks

Hg19::chr14:75078662..75078675,-p6@LTBP2
Hg19::chr14:75078682..75078706,-p5@LTBP2
Hg19::chr14:75078725..75078734,-p15@LTBP2
Hg19::chr14:75079026..75079049,-p8@LTBP2
Hg19::chr14:75079066..75079077,-p13@LTBP2
Hg19::chr14:75079174..75079185,-p22@LTBP2
Hg19::chr14:75079186..75079202,-p11@LTBP2
Hg19::chr14:75079205..75079223,-p7@LTBP2
Hg19::chr14:75079261..75079277,-p9@LTBP2
Hg19::chr14:75079282..75079293,-p21@LTBP2
Hg19::chr14:75079294..75079329,-p2@LTBP2


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>disease_data<br>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell3.78e-22180
mesodermal cell1.10e-21119
embryonic cell4.85e-17248
fibroblast6.54e-1775
contractile cell3.25e-1359
somatic cell2.75e-12591
endothelial cell5.36e-1235
muscle precursor cell5.55e-1257
myoblast5.55e-1257
multi-potent skeletal muscle stem cell5.55e-1257
muscle cell5.38e-1154
vascular associated smooth muscle cell6.39e-1132
meso-epithelial cell8.80e-1144
endothelial cell of vascular tree1.11e-1024
smooth muscle cell1.40e-1042
smooth muscle myoblast1.40e-1042
lining cell5.29e-1057
barrier cell5.29e-1057
blood vessel endothelial cell1.97e-0918
embryonic blood vessel endothelial progenitor cell1.97e-0918
electrically responsive cell1.14e-0860
electrically active cell1.14e-0860
animal cell1.12e-07679
eukaryotic cell1.12e-07679
preadipocyte2.99e-0712
Uber Anatomy
Ontology termp-valuen
vasculature2.21e-2779
vascular system2.21e-2779
vessel3.58e-2369
splanchnic layer of lateral plate mesoderm4.08e-2384
blood vessel1.65e-2260
epithelial tube open at both ends1.65e-2260
blood vasculature1.65e-2260
vascular cord1.65e-2260
circulatory system1.48e-20113
cardiovascular system1.79e-20110
epithelial tube1.16e-19118
artery1.21e-1742
arterial blood vessel1.21e-1742
arterial system1.21e-1742
multi-cellular organism6.06e-17659
cell layer7.80e-17312
epithelium2.91e-16309
anatomical system1.49e-15625
somite2.40e-1583
paraxial mesoderm2.40e-1583
presomitic mesoderm2.40e-1583
presumptive segmental plate2.40e-1583
trunk paraxial mesoderm2.40e-1583
presumptive paraxial mesoderm2.40e-1583
anatomical group3.08e-15626
multilaminar epithelium6.88e-1582
organism subdivision8.46e-15365
trunk mesenchyme2.69e-14143
systemic artery1.49e-1333
systemic arterial system1.49e-1333
unilaminar epithelium5.95e-13138
trunk8.99e-13216
dermomyotome2.02e-1270
surface structure2.83e-1295
anatomical cluster8.10e-12286
skeletal muscle tissue2.35e-1161
striated muscle tissue2.35e-1161
myotome2.35e-1161
anatomical conduit3.91e-11241
muscle tissue3.94e-1163
musculature3.94e-1163
musculature of body3.94e-1163
aorta4.59e-1021
aortic system4.59e-1021
endothelium1.97e-0918
blood vessel endothelium1.97e-0918
cardiovascular system endothelium1.97e-0918
multi-tissue structure4.01e-09347
embryonic structure6.65e-09605
developing anatomical structure6.65e-09605
mesoderm7.42e-09448
mesoderm-derived structure7.42e-09448
presumptive mesoderm7.42e-09448
germ layer7.73e-09604
embryonic tissue7.73e-09604
presumptive structure7.73e-09604
epiblast (generic)7.73e-09604
simple squamous epithelium1.56e-0822
embryo1.95e-08612
squamous epithelium3.37e-0825
subdivision of head4.52e-0848
mesenchyme4.74e-08238
entire embryonic mesenchyme4.74e-08238
integument8.67e-0845
integumental system8.67e-0845
tube3.07e-07194
skin of body9.33e-0740
Disease
Ontology termp-valuen
ovarian cancer1.22e-0714


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
ATF3#467816.33685420073362.24789214598075e-091.92117518685829e-07
CCNT2#90584.608146601427374.03688108190029e-050.000739273756466044
CTCF#1066483.898368271327290.0001406611760594710.00183425053895307
CTCFL#140690712.56593822843822.34732188916212e-071.23377931948769e-05
EGR1#195883.627766614407370.0002392247441646590.00260471153626072
POLR2A#5430112.147453176558070.0002231983422387430.00248540480489093
RAD21#588587.530933742150069.5260786570561e-074.06743306976403e-05
SMC3#912679.574048174048171.48666828013051e-065.73360961996125e-05
TAF1#687282.431306389632940.004204244189139110.0200185583509392
TAF7#687988.31495956721744.42802301552428e-072.11168171560886e-05
YY1#752883.571760545348260.0002682005866906720.00286494845795102
ZBTB7A#5134185.346843133000651.31319566009782e-050.000320816003613932
ZNF143#770289.81881931071121.21663595201433e-077.0007846937975e-06



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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