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{{Coexpression_clusters
{
|full_id=C2079_epididymis_kidney_liver_papillotubular_Hepatocyte_colon_hepatoblastoma
 

Latest revision as of 11:58, 17 September 2013


Full id: C2079_epididymis_kidney_liver_papillotubular_Hepatocyte_colon_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr10:91316455..91316462,-p4@SLC16A12
Hg19::chr3:114464766..114464816,-p@chr3:114464766..114464816
-
Hg19::chr3:114464819..114464840,-p@chr3:114464819..114464840
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Hg19::chr3:114464843..114464849,-p@chr3:114464843..114464849
-


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><br>

Cell Type
Ontology termp-valuen
metabolising cell6.10e-1012
endopolyploid cell6.10e-1012
parenchymal cell6.10e-1012
polyploid cell6.10e-1012
hepatocyte6.10e-1012
kidney cell1.99e-0917
kidney epithelial cell1.99e-0917
epithelial cell of nephron8.77e-0715
Uber Anatomy
Ontology termp-valuen
abdomen element2.93e-1654
abdominal segment element2.93e-1654
trunk region element1.30e-15101
abdominal segment of trunk4.51e-1560
abdomen4.51e-1560
subdivision of trunk9.72e-13112
digestive tract diverticulum3.40e-1223
cavitated compound organ3.46e-1231
sac4.01e-1226
subdivision of digestive tract6.90e-12118
kidney1.17e-1126
kidney mesenchyme1.17e-1126
upper urinary tract1.17e-1126
kidney rudiment1.17e-1126
kidney field1.17e-1126
adult organism1.28e-11114
hepatic diverticulum5.51e-1122
liver primordium5.51e-1122
epithelial sac5.83e-1125
urinary system structure5.85e-1147
epithelium of foregut-midgut junction8.37e-1125
anatomical boundary8.37e-1125
hepatobiliary system8.37e-1125
foregut-midgut junction8.37e-1125
septum transversum8.37e-1125
trunk8.41e-11199
renal system1.29e-1048
digestive system1.73e-10145
digestive tract1.73e-10145
primitive gut1.73e-10145
gut epithelium3.49e-1054
anatomical cluster4.22e-10373
immaterial anatomical entity4.51e-10117
mesenchyme7.17e-10160
entire embryonic mesenchyme7.17e-10160
multi-tissue structure1.86e-09342
compound organ2.51e-0968
endoderm-derived structure3.76e-09160
endoderm3.76e-09160
presumptive endoderm3.76e-09160
liver4.56e-0919
digestive gland4.56e-0919
liver bud4.56e-0919
organism subdivision1.04e-08264
endo-epithelium1.40e-0882
excretory tube3.90e-0816
kidney epithelium3.90e-0816
organ1.54e-07503
intestine3.89e-0717
male genital duct4.07e-073
internal male genitalia4.07e-073
epithelial tube4.98e-07117
anatomical conduit6.04e-07240
nephron epithelium8.77e-0715
renal tubule8.77e-0715
nephron tubule8.77e-0715
nephron8.77e-0715
uriniferous tubule8.77e-0715
nephrogenic mesenchyme8.77e-0715


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.12.78189
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.11.8408
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.14.6858
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0021048
MA0102.21.75932
MA0258.11.88931
MA0259.10.471671
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#105135.978360719368610.007153832484726970.0297144094365415
FOSL2#2355312.69765045342130.000787568572975710.00616542044771832
NR3C1#2908414.9730233311731.98868032687801e-050.000441811922269331
USF1#739134.771124457905970.01370465887188020.048266704927507



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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