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

Latest revision as of 11:39, 17 September 2013


Full id: C1193_mesothelioma_Mesothelial_Retinal_clear_amniotic_serous_Urothelial



Phase1 CAGE Peaks

Hg19::chr14:100003871..100003888,-p@chr14:100003871..100003888
-
Hg19::chr7:76139713..76139729,+p3@UPK3B
Hg19::chr7:76139741..76139750,+p6@UPK3B
Hg19::chr7:76139833..76139844,+p5@UPK3B
Hg19::chr7:76139845..76139887,+p1@UPK3B
Hg19::chr7:76139896..76139907,+p4@UPK3B
Hg19::chr7:76139925..76139937,+p2@UPK3B


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>

Cell Type
Ontology termp-valuen
epithelial cell7.11e-21253
endo-epithelial cell3.66e-1342
mesothelial cell1.23e-1019
endodermal cell2.72e-0958
squamous epithelial cell1.76e-0863
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.28e-11160
endoderm3.28e-11160
presumptive endoderm3.28e-11160
digestive system5.03e-08145
digestive tract5.03e-08145
primitive gut5.03e-08145
endo-epithelium6.61e-0882
anatomical space1.47e-0795
subdivision of digestive tract2.24e-07118
trunk region element2.41e-07101
respiratory tract4.29e-0754
thoracic segment organ7.43e-0735
Disease
Ontology termp-valuen
carcinoma7.20e-14106
adenocarcinoma4.13e-1225
cell type cancer4.53e-11143
cancer2.59e-07235
disease of cellular proliferation7.65e-07239


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)
MA0003.12.0712
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.12.61894
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.11.84146
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.11.47685
MA0067.11.29359
MA0068.12.16244
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.065183
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.12.9044
MA0091.10.505453
MA0092.16.51864
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.695228
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.12.13665
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.11.38735
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.14.76627
MA0146.10.324987
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.23.10611
MA0138.24.08833
MA0002.21.79899
MA0137.20.36398
MA0104.20.636673
MA0047.20.636643
MA0112.20.944394
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.13.65756
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.11.30651
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.24.76472
MA0102.21.51913
MA0258.11.97124
MA0259.10.289405
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
CTCF#1066464.594505462635740.0002478392075687640.00267480407143476
EP300#203365.806235765334176.3256174139893e-050.0010320905438207
MYC#460964.476241604236630.0002883611950910820.00306401005739317
RAD21#588568.875743338962575.20411262905738e-060.00015948131422128
TFAP2C#702269.26505309416594.03752634749879e-060.000130267288911469



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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