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{{Coexpression_clusters
{
|full_id=C1549_breast_liver_Sebocyte_Hepatocyte_pancreas_Bronchial_Prostate

Latest revision as of 11:47, 17 September 2013


Full id: C1549_breast_liver_Sebocyte_Hepatocyte_pancreas_Bronchial_Prostate



Phase1 CAGE Peaks

Hg19::chr9:139379041..139379050,-p@chr9:139379041..139379050
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Hg19::chr9:139379054..139379061,-p@chr9:139379054..139379061
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Hg19::chr9:139379069..139379135,-p@chr9:139379069..139379135
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Hg19::chr9:139379145..139379159,-p@chr9:139379145..139379159
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Hg19::chr9:139379164..139379180,-p@chr9:139379164..139379180
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Hg19::chr9:139379206..139379215,-p@chr9:139379206..139379215
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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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure8.10e-33160
endoderm8.10e-33160
presumptive endoderm8.10e-33160
digestive system1.88e-26145
digestive tract1.88e-26145
primitive gut1.88e-26145
endo-epithelium4.21e-2382
respiratory system4.99e-2174
subdivision of digestive tract1.73e-19118
foregut5.00e-1987
respiratory tract1.68e-1654
gut epithelium8.72e-1454
gland3.13e-1259
exocrine gland6.97e-1231
exocrine system6.97e-1231
respiratory primordium8.16e-1238
endoderm of foregut8.16e-1238
segment of respiratory tract1.20e-1147
organ system subdivision1.04e-10223
trunk region element8.37e-10101
mucosa8.70e-1020
primordium1.20e-09160
immaterial anatomical entity1.20e-09117
epithelial bud3.30e-0937
transitional epithelium4.93e-096
multi-tissue structure7.87e-09342
epithelium of foregut-midgut junction1.22e-0825
anatomical boundary1.22e-0825
hepatobiliary system1.22e-0825
foregut-midgut junction1.22e-0825
septum transversum1.22e-0825
organism subdivision2.36e-08264
urothelium2.55e-085
epithelial fold3.66e-0847
subdivision of trunk4.82e-08112
thoracic cavity element6.40e-0834
thoracic cavity6.40e-0834
orifice8.67e-0836
thoracic segment organ1.43e-0735
oral opening3.10e-0722
mammary gland4.82e-074
mammary bud4.82e-074
mammary ridge4.82e-074
mammary placode4.82e-074
thoracic segment of trunk8.92e-0752
respiratory system epithelium9.19e-0728
Disease
Ontology termp-valuen
carcinoma5.47e-26106
cell type cancer9.08e-17143
squamous cell carcinoma1.38e-1314
cancer6.51e-08235
disease of cellular proliferation1.93e-07239
disease of anatomical entity2.13e-0739


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)
MA0003.11.73878
MA0004.13.45359
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
MA0017.10.432438
MA0019.10.7124
MA0024.12.14259
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.15.26721
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.13.5183
MA0056.10
MA0057.10.882847
MA0058.19.0515
MA0059.110.4065
MA0060.11.35477
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.12.56931
MA0072.11.00572
MA0073.10.120085
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.12.29259
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.15.90743
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.13.26878
MA0117.11.07516
MA0119.12.92176
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.093337
MA0147.14.27395
MA0148.13.56798
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.200862
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.23.79531
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.11.18186
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.22.24517
MA0102.21.58513
MA0258.10.788656
MA0259.12.42942
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
FOXA1#3169611.08141974938555.39600313513231e-072.51137776929627e-05
MXI1#460169.96157162875931.02262624227062e-064.30827196920133e-05
MYC#460965.22228187160944.92821127172503e-050.000854979164464603
POLR2A#543062.147453176558070.01019570676818780.0380799420363611
USF1#739166.361499277207961.50818327938273e-050.000357172683708511



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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