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Coexpression cluster:C3303: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3303_Smooth_Adipocyte_smooth_Mallassezderived_Fibroblast_Endothelial_Aortic
|id=C3303
}}

Latest revision as of 12:23, 17 September 2013


Full id: C3303_Smooth_Adipocyte_smooth_Mallassezderived_Fibroblast_Endothelial_Aortic



Phase1 CAGE Peaks

Hg19::chr12:56552128..56552162,+p1@MYL6
Hg19::chr12:56554057..56554082,-p@chr12:56554057..56554082
-
Hg19::chr17:69617073..69617130,+p1@ENST00000412707
p1@ENST00000545441


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:0030898actin-dependent ATPase activity0.00269830056124651
GO:0030049muscle filament sliding0.00269830056124651
GO:0033275actin-myosin filament sliding0.00269830056124651
GO:0016461unconventional myosin complex0.00283321558930884
GO:0030048actin filament-based movement0.00518073707759331
GO:0008307structural constituent of muscle0.0113328623572354
GO:0007519skeletal muscle development0.01549595465173
GO:0014706striated muscle development0.017808783704227
GO:0016459myosin complex0.0192478773368918
GO:0003012muscle system process0.02320538482672
GO:0006936muscle contraction0.02320538482672
GO:0007517muscle development0.02320538482672
GO:0030705cytoskeleton-dependent intracellular transport0.0244092420001992
GO:0030029actin filament-based process0.0300667776824612
GO:0015629actin cytoskeleton0.0319478786451587



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>

Uber Anatomy
Ontology termp-valuen
vasculature1.30e-2278
vascular system1.30e-2278
epithelial tube open at both ends1.09e-2159
blood vessel1.09e-2159
blood vasculature1.09e-2159
vascular cord1.09e-2159
splanchnic layer of lateral plate mesoderm1.68e-2183
vessel7.22e-2168
epithelial vesicle5.64e-2078
artery4.08e-1942
arterial blood vessel4.08e-1942
arterial system4.08e-1942
epithelial tube8.61e-19117
somite4.88e-1871
presomitic mesoderm4.88e-1871
presumptive segmental plate4.88e-1871
dermomyotome4.88e-1871
trunk paraxial mesoderm4.88e-1871
dense mesenchyme tissue4.96e-1873
cardiovascular system6.58e-18109
mesoderm7.40e-18315
mesoderm-derived structure7.40e-18315
presumptive mesoderm7.40e-18315
muscle tissue9.86e-1864
musculature9.86e-1864
musculature of body9.86e-1864
paraxial mesoderm1.51e-1772
presumptive paraxial mesoderm1.51e-1772
circulatory system1.75e-17112
skeletal muscle tissue1.95e-1762
striated muscle tissue1.95e-1762
myotome1.95e-1762
multilaminar epithelium4.57e-1783
unilaminar epithelium1.48e-15148
trunk mesenchyme3.66e-14122
systemic artery3.67e-1433
systemic arterial system3.67e-1433
mesenchyme4.00e-13160
entire embryonic mesenchyme4.00e-13160
trunk1.56e-10199
multi-cellular organism3.31e-10656
organism subdivision1.26e-09264
lateral plate mesoderm1.77e-09203
musculoskeletal system1.92e-08167
aorta7.65e-0821
aortic system7.65e-0821
anatomical system8.66e-08624
anatomical group9.04e-08625
blood vessel endothelium8.58e-0718
endothelium8.58e-0718
cardiovascular system endothelium8.58e-0718


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.112.1974
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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