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Coexpression cluster:C2181: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2181_Smooth_Fibroblast_leiomyoma_mesenchymal_hepatic_normal_Preadipocyte
|id=C2181
}}

Latest revision as of 12:00, 17 September 2013


Full id: C2181_Smooth_Fibroblast_leiomyoma_mesenchymal_hepatic_normal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr12:106633037..106633066,-p10@CKAP4
Hg19::chr12:106641713..106641725,-p4@CKAP4
Hg19::chr12:106641728..106641805,-p1@CKAP4
Hg19::chr21:46707793..46707815,-p1@POFUT2


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

GO IDGO nameFDR corrected p-value
GO:0046922peptide-O-fucosyltransferase activity0.00400323791041627
GO:0033116ER-Golgi intermediate compartment membrane0.0072041312773884
GO:0005783endoplasmic reticulum0.0072041312773884
GO:0006004fucose metabolic process0.0072041312773884
GO:0008417fucosyltransferase activity0.0072041312773884
GO:0005793ER-Golgi intermediate compartment0.0143362791822346



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
mesodermal cell3.04e-25121
contractile cell6.87e-2159
muscle precursor cell8.50e-2158
myoblast8.50e-2158
multi-potent skeletal muscle stem cell8.50e-2158
fibroblast1.83e-2076
smooth muscle cell6.44e-2043
smooth muscle myoblast6.44e-2043
muscle cell7.30e-2055
somatic cell3.10e-19588
animal cell7.20e-17679
eukaryotic cell7.20e-17679
vascular associated smooth muscle cell9.78e-1732
electrically responsive cell2.10e-1561
electrically active cell2.10e-1561
embryonic cell6.36e-14250
non-terminally differentiated cell2.59e-13106
multi fate stem cell1.29e-10427
somatic stem cell4.91e-10433
stem cell6.26e-09441
native cell5.71e-08722
lining cell6.78e-0758
barrier cell6.78e-0758
skin fibroblast6.88e-0723
cardiocyte7.51e-0716
Uber Anatomy
Ontology termp-valuen
epithelial vesicle5.68e-2278
vasculature1.07e-2178
vascular system1.07e-2178
multilaminar epithelium2.32e-2083
vessel2.77e-2068
epithelial tube2.87e-20117
somite8.78e-2071
presomitic mesoderm8.78e-2071
presumptive segmental plate8.78e-2071
dermomyotome8.78e-2071
trunk paraxial mesoderm8.78e-2071
dense mesenchyme tissue1.15e-1973
trunk mesenchyme2.19e-19122
splanchnic layer of lateral plate mesoderm2.27e-1983
paraxial mesoderm3.98e-1972
presumptive paraxial mesoderm3.98e-1972
artery4.15e-1942
arterial blood vessel4.15e-1942
arterial system4.15e-1942
unilaminar epithelium9.32e-19148
epithelial tube open at both ends1.10e-1859
blood vessel1.10e-1859
blood vasculature1.10e-1859
vascular cord1.10e-1859
skeletal muscle tissue1.84e-1862
striated muscle tissue1.84e-1862
myotome1.84e-1862
mesenchyme3.41e-18160
entire embryonic mesenchyme3.41e-18160
muscle tissue1.02e-1764
musculature1.02e-1764
musculature of body1.02e-1764
cardiovascular system4.31e-17109
circulatory system9.72e-17112
mesoderm7.87e-16315
mesoderm-derived structure7.87e-16315
presumptive mesoderm7.87e-16315
systemic artery1.61e-1533
systemic arterial system1.61e-1533
organism subdivision2.03e-13264
trunk2.52e-13199
multi-cellular organism2.04e-12656
anatomical group1.61e-11625
anatomical system3.48e-11624
cell layer6.45e-09309
aorta7.24e-0921
aortic system7.24e-0921
epithelium1.13e-08306
musculoskeletal system1.94e-08167
surface structure3.72e-0799
lateral plate mesoderm4.48e-07203
multi-tissue structure5.36e-07342
developing anatomical structure9.13e-07581
Disease
Ontology termp-valuen
ovarian cancer4.69e-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)
MA0003.12.92335
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.13.08565
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
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
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
MA0105.11.90157
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.13.58384
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.01147
MA0138.22.1393
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.533581
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.13.50007
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.26.45898
MA0102.21.75932
MA0258.10.418966
MA0259.12.06681
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

No analysis results for this cluster

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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