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Coexpression cluster:C4549: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4549_cholangiocellular_Preadipocyte_Fibroblast_Adipocyte_mesenchymal_Aortic_Smooth
|full_id=C4549_cholangiocellular_Preadipocyte_Fibroblast_Adipocyte_mesenchymal_Aortic_Smooth
|id=C4549
|id=C4549

Revision as of 17:38, 12 September 2012


Full id: C4549_cholangiocellular_Preadipocyte_Fibroblast_Adipocyte_mesenchymal_Aortic_Smooth



Phase1 CAGE Peaks

Hg19::chr6:116832767..116832787,+p3@FAM26E
Hg19::chr6:116832789..116832811,+p2@FAM26E
Hg19::chr6:116832823..116832853,+p1@FAM26E


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>


Uber Anatomy
Ontology termp-valuen
circulatory system4.59e-26113
cardiovascular system1.27e-25110
splanchnic layer of lateral plate mesoderm2.63e-2484
vasculature5.12e-2279
vascular system5.12e-2279
somite5.37e-2283
paraxial mesoderm5.37e-2283
presomitic mesoderm5.37e-2283
presumptive segmental plate5.37e-2283
trunk paraxial mesoderm5.37e-2283
presumptive paraxial mesoderm5.37e-2283
vessel3.28e-2069
blood vessel3.50e-1960
epithelial tube open at both ends3.50e-1960
blood vasculature3.50e-1960
vascular cord3.50e-1960
dermomyotome9.31e-1970
muscle tissue2.10e-1863
musculature2.10e-1863
musculature of body2.10e-1863
skeletal muscle tissue3.98e-1861
striated muscle tissue3.98e-1861
myotome3.98e-1861
artery7.14e-1842
arterial blood vessel7.14e-1842
arterial system7.14e-1842
multilaminar epithelium5.85e-1782
systemic artery7.30e-1533
systemic arterial system7.30e-1533
trunk mesenchyme7.16e-14143
epithelial tube1.72e-13118
organism subdivision2.12e-13365
unilaminar epithelium2.43e-12138
anatomical cluster3.07e-10286
surface structure3.20e-1095
aorta3.30e-1021
aortic system3.30e-1021
multi-cellular organism8.68e-10659
trunk9.62e-10216
cell layer1.76e-09312
primary circulatory organ1.93e-0927
heart3.47e-0924
primitive heart tube3.47e-0924
primary heart field3.47e-0924
anterior lateral plate mesoderm3.47e-0924
heart tube3.47e-0924
heart primordium3.47e-0924
cardiac mesoderm3.47e-0924
cardiogenic plate3.47e-0924
heart rudiment3.47e-0924
epithelium7.46e-09309
integument1.70e-0845
integumental system1.70e-0845
anatomical conduit1.80e-08241
anatomical system3.93e-08625
anatomical group4.23e-08626
multi-tissue structure9.30e-08347
skin of body3.93e-0740
smooth muscle tissue7.06e-0715
Disease
Ontology termp-valuen
ovarian cancer5.60e-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
CEBPB#105137.971147625824820.001974187055288560.0115683174475274
CTCF#1066435.360256373075030.0064925092527670.0280995886556601
EP300#203336.77394172622320.003216880500103790.0168244670514467
GATA2#2624312.7449317335540.0004829527704283790.00438715355229795
JUN#3725312.51282919233630.0005103313992726250.00446087219690607
JUNB#3726330.61063265982113.4847716247536e-050.000682313580273044
JUND#372736.994663941871030.002921845042734990.0157539790613423
RAD21#5885310.35503389545630.0009004912073565420.00667848325558229
SETDB1#9869340.32002617801051.52461559299059e-050.000359758987610358
SMC3#9126315.04493284493280.0002935825420371870.00310558767424509
TAL1#6886329.86861667744023.75103522793067e-050.000722261003263
TRIM28#10155318.59052504526250.0001555969297255280.00197813606130303



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.