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{{Coexpression_clusters
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|full_id=C2062_Myoblast_mesenchymal_Smooth_leiomyoma_Preadipocyte_Aortic_Fibroblast
|id=C2062
}}

Latest revision as of 11:58, 17 September 2013


Full id: C2062_Myoblast_mesenchymal_Smooth_leiomyoma_Preadipocyte_Aortic_Fibroblast



Phase1 CAGE Peaks

Hg19::chr10:49813013..49813032,-p3@ARHGAP22
Hg19::chr10:49813051..49813064,-p4@ARHGAP22
Hg19::chr10:49813077..49813087,-p8@ARHGAP22
Hg19::chr10:49813090..49813198,-p1@ARHGAP22


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
muscle precursor cell3.18e-2358
myoblast3.18e-2358
multi-potent skeletal muscle stem cell3.18e-2358
mesodermal cell1.16e-22121
contractile cell3.43e-2259
vascular associated smooth muscle cell5.24e-2232
smooth muscle cell1.71e-2143
smooth muscle myoblast1.71e-2143
muscle cell7.03e-2155
somatic cell1.69e-19588
fibroblast4.35e-1876
multi fate stem cell5.39e-18427
electrically responsive cell5.41e-1761
electrically active cell5.41e-1761
somatic stem cell6.43e-17433
stem cell1.51e-15441
non-terminally differentiated cell9.42e-15106
skin fibroblast9.31e-1223
aortic smooth muscle cell3.64e-1010
animal cell6.54e-10679
eukaryotic cell6.54e-10679
endothelial cell of vascular tree5.81e-0924
embryonic cell1.63e-08250
blood vessel endothelial cell1.39e-0718
embryonic blood vessel endothelial progenitor cell1.39e-0718
endothelial cell3.44e-0736
Uber Anatomy
Ontology termp-valuen
artery3.76e-3142
arterial blood vessel3.76e-3142
arterial system3.76e-3142
vessel2.40e-3068
epithelial tube open at both ends1.63e-2859
blood vessel1.63e-2859
blood vasculature1.63e-2859
vascular cord1.63e-2859
vasculature5.27e-2778
vascular system5.27e-2778
epithelial vesicle1.03e-2578
dense mesenchyme tissue2.48e-2573
systemic artery3.31e-2533
systemic arterial system3.31e-2533
paraxial mesoderm3.84e-2572
presumptive paraxial mesoderm3.84e-2572
somite4.73e-2571
presomitic mesoderm4.73e-2571
presumptive segmental plate4.73e-2571
dermomyotome4.73e-2571
trunk paraxial mesoderm4.73e-2571
multilaminar epithelium2.84e-2283
splanchnic layer of lateral plate mesoderm3.27e-2183
skeletal muscle tissue2.12e-2062
striated muscle tissue2.12e-2062
myotome2.12e-2062
muscle tissue3.89e-1964
musculature3.89e-1964
musculature of body3.89e-1964
cardiovascular system2.00e-18109
circulatory system3.08e-17112
epithelial tube1.08e-16117
aorta6.71e-1621
aortic system6.71e-1621
unilaminar epithelium6.90e-15148
mesoderm9.77e-15315
mesoderm-derived structure9.77e-15315
presumptive mesoderm9.77e-15315
musculoskeletal system4.42e-13167
trunk mesenchyme4.12e-12122
cell layer1.93e-11309
epithelium4.64e-11306
anatomical conduit1.14e-10240
tube2.62e-10192
blood vessel smooth muscle3.64e-1010
arterial system smooth muscle3.64e-1010
artery smooth muscle tissue3.64e-1010
aorta smooth muscle tissue3.64e-1010
integument5.85e-1046
integumental system5.85e-1046
anatomical system7.32e-10624
anatomical group9.71e-10625
mesenchyme1.05e-09160
entire embryonic mesenchyme1.05e-09160
skin of body4.20e-0941
surface structure1.11e-0899
multi-cellular organism1.72e-08656
lateral plate mesoderm2.12e-08203
smooth muscle tissue5.91e-0815
blood vessel endothelium1.39e-0718
endothelium1.39e-0718
cardiovascular system endothelium1.39e-0718
Disease
Ontology termp-valuen
ovarian cancer4.06e-0814


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.16.90671
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.13.49299
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.13.20115
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.11.91637
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.28.68914
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.23.97967
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



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
EGR1#195844.988179094810140.001615011500076050.0101224380997685



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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