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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0.

Latest revision as of 11:47, 17 September 2013


Full id: C1585_nonsmall_hepatoma_mucinous_bile_lung_Adipocyte_mature



Phase1 CAGE Peaks

Hg19::chr10:5005598..5005621,+p1@AKR1C1
Hg19::chr10:5060113..5060122,-p4@AKR1C2
Hg19::chr10:5060148..5060171,-p2@AKR1C2
Hg19::chr10:5060184..5060198,-p3@AKR1C2
Hg19::chr10:5136595..5136628,+p1@AKR1C3


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

p.valueFDRnGenesnPathwayName
7.54806151097432e-091.59264097881558e-06357Steroid hormone biosynthesis (KEGG):00140
1.47440005351926e-082.33323808469424e-06371Metabolism of xenobiotics by cytochrome P450 (KEGG):00980
2.16690761080603e-111.37165251764022e-0839Benzo(a)pyrene metabolism (Wikipathways):WP696
2.26486989237789e-072.8673252837504e-053175metapathway biotransformation (Wikipathways):WP702
1.73517139063789e-050.001830605817122973740TGF beta receptor down reg. targets (Netpath):NetPath_7
3.43093705044287e-101.08589157646517e-07321{POU2F1,21} (Static Module):NA



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:0047115trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity1.05602779107617e-11
GO:0016628oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor2.95687781501328e-09
GO:0016229steroid dehydrogenase activity1.74596594791261e-08
GO:0032052bile acid binding7.17465281257153e-08
GO:00470263-alpha-hydroxysteroid dehydrogenase (A-specific) activity7.17465281257153e-08
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors1.6171481578645e-07
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor9.00496018006475e-07
GO:0016614oxidoreductase activity, acting on CH-OH group of donors9.70397137567286e-07
GO:0004033aldo-keto reductase activity2.63018975102282e-06
GO:0031406carboxylic acid binding3.26369824148814e-06
GO:0032787monocarboxylic acid metabolic process3.74303770407995e-06
GO:0006693prostaglandin metabolic process3.75179054980983e-06
GO:0006692prostanoid metabolic process3.75179054980983e-06
GO:0006690icosanoid metabolic process3.13595372768503e-05
GO:0044255cellular lipid metabolic process5.24142597046853e-05
GO:0019752carboxylic acid metabolic process5.24142597046853e-05
GO:0006082organic acid metabolic process5.24142597046853e-05
GO:0006629lipid metabolic process8.25175891835759e-05
GO:0007586digestion8.41483072985558e-05
GO:004700620-alpha-hydroxysteroid dehydrogenase activity0.0002877314018207
GO:0047017prostaglandin-F synthase activity0.0002877314018207
GO:0006631fatty acid metabolic process0.0002877314018207
GO:0016491oxidoreductase activity0.0002877314018207
GO:0008202steroid metabolic process0.000368383180518114
GO:00470423-alpha-hydroxysteroid dehydrogenase (B-specific) activity0.00048744591208611
GO:0047045testosterone 17-beta-dehydrogenase (NADP+) activity0.000703026292878017
GO:0050327testosterone 17-beta-dehydrogenase activity0.000902624470962375
GO:0015721bile acid and bile salt transport0.00108795282557785
GO:0030299cholesterol absorption0.00162453274055371
GO:0044241lipid digestion0.00162453274055371
GO:0050892intestinal absorption0.00196504487007652
GO:0015718monocarboxylic acid transport0.00257815269091689
GO:0008206bile acid metabolic process0.00257815269091689
GO:0042632cholesterol homeostasis0.00257815269091689
GO:0055092sterol homeostasis0.00257815269091689
GO:0006118electron transport0.00257815269091689
GO:0055088lipid homeostasis0.00279828446182722
GO:0022600digestive system process0.0030450126061026
GO:0006091generation of precursor metabolites and energy0.00396795665993615
GO:0006805xenobiotic metabolic process0.00471810220199635
GO:0009410response to xenobiotic stimulus0.00504803476275117
GO:0051260protein homooligomerization0.00594117466120264
GO:0051259protein oligomerization0.00876985438476458
GO:0046942carboxylic acid transport0.0133665226178137
GO:0015849organic acid transport0.0133665226178137
GO:0005737cytoplasm0.0160193622354137
GO:0048878chemical homeostasis0.038806504830292
GO:0006461protein complex assembly0.0427312690939316
GO:0032501multicellular organismal process0.0494503357430177



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
fat cell1.05e-1015
fibroblast of choroid plexus4.98e-082
Disease
Ontology termp-valuen
respiratory system cancer3.30e-0816
carcinoma3.99e-07106


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.860776
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.11.28241
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.11.52322
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.11.87149
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.77901
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.11.05321
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.146371
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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

No analysis results for this cluster

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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