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Coexpression cluster:C3236: Difference between revisions

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{{Coexpression_clusters
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primary transcript binding!0.00571041708603294!284119$GO:0006361!transcription initiation from RNA polymerase I promoter!0.00571041708603294!284119$GO:0003716!RNA polymerase I transcription termination factor activity!0.00571041708603294!284119$GO:0003715!transcription termination factor activity!0.00856512133858862!284119$GO:0006353!transcription termination!0.011990110916016!284119$GO:0006360!transcription from RNA polymerase I promoter!0.0142726809766186!284119$GO:0016599!caveolar membrane!0.0225641601782574!284119$GO:0043624!cellular protein complex disassembly!0.0225641601782574!284119$GO:0043241!protein complex disassembly!0.0225641601782574!284119$GO:0032984!macromolecular complex disassembly!0.0225641601782574!284119$GO:0005901!caveola!0.0225641601782574!284119$GO:0019843!rRNA binding!0.025671166149659!284119$GO:0022411!cellular component 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|full_id=C3236_Mesenchymal_Endothelial_Smooth_Hair_Fibroblast_Preadipocyte_Renal
|id=C3236
}}

Latest revision as of 12:22, 17 September 2013


Full id: C3236_Mesenchymal_Endothelial_Smooth_Hair_Fibroblast_Preadipocyte_Renal



Phase1 CAGE Peaks

Hg19::chr12:109915098..109915131,-p1@KCTD10
Hg19::chr17:40575264..40575282,-p1@PTRF
Hg19::chr20:35090158..35090240,+p2@DLGAP4


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:0042134rRNA primary transcript binding0.00571041708603294
GO:0006361transcription initiation from RNA polymerase I promoter0.00571041708603294
GO:0003716RNA polymerase I transcription termination factor activity0.00571041708603294
GO:0003715transcription termination factor activity0.00856512133858862
GO:0006353transcription termination0.011990110916016
GO:0006360transcription from RNA polymerase I promoter0.0142726809766186
GO:0016599caveolar membrane0.0225641601782574
GO:0043624cellular protein complex disassembly0.0225641601782574
GO:0043241protein complex disassembly0.0225641601782574
GO:0032984macromolecular complex disassembly0.0225641601782574
GO:0005901caveola0.0225641601782574
GO:0019843rRNA binding0.025671166149659
GO:0022411cellular component disassembly0.0322411709060457



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
mesodermal cell6.43e-34121
fibroblast4.02e-2276
embryonic cell1.62e-21250
somatic cell1.05e-19588
lining cell9.82e-1758
barrier cell9.82e-1758
contractile cell1.61e-1659
muscle precursor cell3.79e-1658
myoblast3.79e-1658
multi-potent skeletal muscle stem cell3.79e-1658
smooth muscle cell1.44e-1543
smooth muscle myoblast1.44e-1543
muscle cell1.47e-1555
animal cell2.45e-15679
eukaryotic cell2.45e-15679
meso-epithelial cell3.07e-1545
endothelial cell1.08e-1436
endothelial cell of vascular tree6.22e-1324
vascular associated smooth muscle cell1.13e-1232
non-terminally differentiated cell5.21e-12106
electrically responsive cell1.19e-1161
electrically active cell1.19e-1161
blood vessel endothelial cell3.35e-1118
embryonic blood vessel endothelial progenitor cell3.35e-1118
skin fibroblast1.74e-0823
squamous epithelial cell3.13e-0763
endothelial cell of artery8.05e-079
Uber Anatomy
Ontology termp-valuen
vasculature4.87e-2978
vascular system4.87e-2978
vessel5.40e-2768
splanchnic layer of lateral plate mesoderm3.08e-2583
epithelial tube open at both ends6.65e-2559
blood vessel6.65e-2559
blood vasculature6.65e-2559
vascular cord6.65e-2559
epithelial tube5.62e-24117
unilaminar epithelium2.92e-21148
epithelial vesicle4.40e-2178
cardiovascular system1.28e-19109
circulatory system1.95e-19112
artery2.20e-1942
arterial blood vessel2.20e-1942
arterial system2.20e-1942
multilaminar epithelium6.74e-1983
trunk mesenchyme3.91e-18122
organism subdivision4.12e-18264
mesenchyme7.13e-18160
entire embryonic mesenchyme7.13e-18160
somite9.27e-1871
presomitic mesoderm9.27e-1871
presumptive segmental plate9.27e-1871
dermomyotome9.27e-1871
trunk paraxial mesoderm9.27e-1871
paraxial mesoderm4.59e-1772
presumptive paraxial mesoderm4.59e-1772
dense mesenchyme tissue4.60e-1773
trunk1.56e-16199
muscle tissue2.73e-1564
musculature2.73e-1564
musculature of body2.73e-1564
skeletal muscle tissue2.90e-1562
striated muscle tissue2.90e-1562
myotome2.90e-1562
systemic artery7.90e-1533
systemic arterial system7.90e-1533
mesoderm1.16e-14315
mesoderm-derived structure1.16e-14315
presumptive mesoderm1.16e-14315
multi-cellular organism9.01e-14656
anatomical system1.78e-13624
cell layer2.13e-13309
anatomical group3.60e-13625
epithelium9.18e-13306
surface structure4.26e-1299
blood vessel endothelium3.35e-1118
endothelium3.35e-1118
cardiovascular system endothelium3.35e-1118
squamous epithelium9.50e-1125
simple squamous epithelium1.73e-1022
aorta6.33e-1021
aortic system6.33e-1021
integument8.03e-0946
integumental system8.03e-0946
anatomical conduit1.56e-08240
skin of body7.81e-0841
anatomical cluster1.06e-07373
multi-tissue structure1.88e-07342
endothelial tube8.05e-079
arterial system endothelium8.05e-079
endothelium of artery8.05e-079


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
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
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.12.75836
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.846801
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
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
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
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.25.16052
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ZZZ3#26009179.80440414507770.0124784379082580.0451540287125132



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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