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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:30, 17 September 2013


Full id: C773_Smooth_mesenchymal_Hair_Lymphatic_Preadipocyte_Aortic_anaplastic



Phase1 CAGE Peaks

Hg19::chr4:74735102..74735117,+p1@CXCL1
Hg19::chr4:74735383..74735394,+p@chr4:74735383..74735394
+
Hg19::chr4:74735431..74735449,+p@chr4:74735431..74735449
+
Hg19::chr4:74735641..74735656,+p@chr4:74735641..74735656
+
Hg19::chr4:74736251..74736276,+p@chr4:74736251..74736276
+
Hg19::chr4:74736294..74736305,+p@chr4:74736294..74736305
+
Hg19::chr4:74736340..74736359,+p@chr4:74736340..74736359
+
Hg19::chr4:74736382..74736398,+p@chr4:74736382..74736398
+
Hg19::chr4:74736459..74736475,+p@chr4:74736459..74736475
+
Hg19::chr4:74736642..74736654,+p@chr4:74736642..74736654
+
Hg19::chr4:74810127..74810130,-p1@ENST00000502804


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:0008009chemokine activity0.0322890344084268
GO:0042379chemokine receptor binding0.0322890344084268
GO:0001664G-protein-coupled receptor binding0.0322890344084268
GO:0042330taxis0.0322890344084268
GO:0006935chemotaxis0.0322890344084268
GO:0007626locomotory behavior0.0322890344084268
GO:0008285negative regulation of cell proliferation0.0322890344084268
GO:0030036actin cytoskeleton organization and biogenesis0.0322890344084268
GO:0008083growth factor activity0.0322890344084268
GO:0030029actin filament-based process0.0322890344084268
GO:0006954inflammatory response0.0322890344084268
GO:0007610behavior0.0322890344084268
GO:0005125cytokine activity0.0322890344084268
GO:0009611response to wounding0.0396907747556811
GO:0008047enzyme activator activity0.0396907747556811
GO:0042127regulation of cell proliferation0.0396907747556811
GO:0005615extracellular space0.0419757447309549
GO:0006952defense response0.0419757447309549
GO:0042221response to chemical stimulus0.0419757447309549
GO:0009605response to external stimulus0.0428558813140233
GO:0007010cytoskeleton organization and biogenesis0.043859649122807
GO:0007399nervous system development0.043859649122807
GO:0008283cell proliferation0.043859649122807



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
artery3.37e-2942
arterial blood vessel3.37e-2942
arterial system3.37e-2942
systemic artery2.47e-2333
systemic arterial system2.47e-2333
vasculature1.64e-2278
vascular system1.64e-2278
vessel3.36e-2168
splanchnic layer of lateral plate mesoderm4.21e-2183
epithelial tube open at both ends1.92e-2059
blood vessel1.92e-2059
blood vasculature1.92e-2059
vascular cord1.92e-2059
cardiovascular system5.26e-20109
circulatory system5.66e-19112
multilaminar epithelium3.50e-1783
skeletal muscle tissue3.66e-1662
striated muscle tissue3.66e-1662
myotome3.66e-1662
muscle tissue2.78e-1564
musculature2.78e-1564
musculature of body2.78e-1564
somite1.14e-1471
presomitic mesoderm1.14e-1471
presumptive segmental plate1.14e-1471
dermomyotome1.14e-1471
trunk paraxial mesoderm1.14e-1471
paraxial mesoderm2.70e-1472
presumptive paraxial mesoderm2.70e-1472
mesoderm3.99e-14315
mesoderm-derived structure3.99e-14315
presumptive mesoderm3.99e-14315
dense mesenchyme tissue6.25e-1473
epithelial vesicle4.19e-1378
musculoskeletal system6.95e-13167
lateral plate mesoderm2.44e-12203
epithelial tube3.80e-12117
unilaminar epithelium7.52e-11148
blood vessel smooth muscle1.16e-1010
arterial system smooth muscle1.16e-1010
artery smooth muscle tissue1.16e-1010
aorta smooth muscle tissue1.16e-1010
aorta2.84e-1021
aortic system2.84e-1021
smooth muscle tissue1.18e-0815
developing anatomical structure4.91e-08581
embryonic structure5.47e-08564
trunk mesenchyme5.57e-08122
thoracic segment blood vessel7.48e-085
subclavian artery7.48e-085
embryo3.30e-07592
germ layer4.60e-07560
germ layer / neural crest4.60e-07560
embryonic tissue4.60e-07560
presumptive structure4.60e-07560
germ layer / neural crest derived structure4.60e-07560
epiblast (generic)4.60e-07560
anatomical system7.08e-07624
anatomical group8.34e-07625
Disease
Ontology termp-valuen
female reproductive organ cancer1.15e-0727
ovarian cancer3.00e-0714
reproductive organ cancer7.83e-0729


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)
MA0003.10.486434
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.11.85742
MA0014.10.00227771
MA0017.11.9612
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.637069
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.895841
MA0043.10.790919
MA0046.10.779945
MA0048.11.12059
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.11.40057
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.12.24862
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.556338
MA0069.11.82765
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.13.35264
MA0074.13.96542
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.11.34305
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.248289
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.852371
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.11.81378
MA0103.11.11087
MA0105.10.360248
MA0106.10.482519
MA0107.11.47931
MA0108.21.52518
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.11.49522
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.822953
MA0146.10.0381286
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.320507
MA0035.20.404774
MA0039.20.556508
MA0138.20.534556
MA0002.20.358551
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.487949
MA0065.20.0286783
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.989789
MA0155.10.245306
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.948902
MA0160.10.386031
MA0161.10
MA0162.10.0266618
MA0163.10.0519618
MA0164.13.23562
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.20.0134506
MA0102.22.94735
MA0258.10.831523
MA0259.10.168926
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
CEBPB#105153.623248920829460.0074439847494370.0307095245396765
POLR2A#5430101.952230160507340.00304073181841430.0161359174017261
STAT3#677454.781574998706470.002192062661377620.0126365751665076



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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