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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4196_Fibroblast_Smooth_mesenchymal_giant_embryonic_Skeletal_Placental
|full_id=C4196_Fibroblast_Smooth_mesenchymal_giant_embryonic_Skeletal_Placental
|id=C4196
|id=C4196

Revision as of 17:14, 12 September 2012


Full id: C4196_Fibroblast_Smooth_mesenchymal_giant_embryonic_Skeletal_Placental



Phase1 CAGE Peaks

Hg19::chr2:228682784..228682794,-p@chr2:228682784..228682794
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Hg19::chr2:228682809..228682833,-p@chr2:228682809..228682833
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Hg19::chr2:228682869..228682884,-p@chr2:228682869..228682884
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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>


Cell Type
Ontology termp-valuen
animal cell3.27e-17679
eukaryotic cell3.27e-17679
somatic cell1.14e-13591
native cell3.98e-11722
cardiocyte1.38e-0816
fibroblast7.82e-0875
non-terminally differentiated cell1.16e-07180
somatic stem cell1.46e-07436
multi fate stem cell3.80e-07430
muscle precursor cell4.04e-0757
myoblast4.04e-0757
multi-potent skeletal muscle stem cell4.04e-0757
Uber Anatomy
Ontology termp-valuen
mesoderm2.14e-12448
mesoderm-derived structure2.14e-12448
presumptive mesoderm2.14e-12448
germ layer2.78e-09604
embryonic tissue2.78e-09604
presumptive structure2.78e-09604
epiblast (generic)2.78e-09604
trunk2.86e-09216
embryonic structure3.64e-09605
developing anatomical structure3.64e-09605
somite1.31e-0883
paraxial mesoderm1.31e-0883
presomitic mesoderm1.31e-0883
presumptive segmental plate1.31e-0883
trunk paraxial mesoderm1.31e-0883
presumptive paraxial mesoderm1.31e-0883
embryo2.27e-08612
multi-cellular organism3.89e-08659
trunk mesenchyme6.34e-08143
mesenchyme1.86e-07238
entire embryonic mesenchyme1.86e-07238
dermomyotome2.06e-0770
multilaminar epithelium7.51e-0782


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
CEBPB#105137.971147625824820.001974187055288560.0115482313132789
CHD2#1106310.34402283411690.0009033701102746880.00661666813570224
CTCF#1066435.360256373075030.0064925092527670.0280194699937906
EBF1#187938.9064668465690.00141523283560980.00917135158341104
EP300#203336.77394172622320.003216880500103790.0167832841717624
FOS#235338.99795530889440.001372499272417130.0089943183479935
FOSL2#2355316.93020060456170.0002060162053171620.00243532840601235
FOXA1#3169311.08141974938550.000734755275698670.00582444829136192
GATA2#2624312.7449317335540.0004829527704283790.00437649495798434
GTF2F1#2962312.73966087675770.0004835525047438590.00434872470876982
JUN#3725312.51282919233630.0005103313992726250.00445007105357215
JUND#372736.994663941871030.002921845042734990.0157109908056531
NR3C1#2908314.9730233311730.0002978331194675480.003095063996425
PRDM1#6393131.8309557774614.35536935195671e-072.08274001716578e-05
RAD21#5885310.35503389545630.0009004912073565420.00665815229770689
RXRA#6256320.07461713913330.0001235730348432220.00165480756327623
SIN3A#2594235.408884726815140.006318961977991520.0277509806155947
STAT3#6774310.51946499715420.0008589184530415310.00643828208693063
TCF7L2#6934310.77017656313730.0008003181298398380.00615269968070246
TFAP2A#7020316.5186343730450.0002218033880766340.00248764218721387
TFAP2C#7022310.80922860986020.0007916746575753130.00617119790733752
TRIM28#10155318.59052504526250.0001555969297255280.00197453071003698



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.