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Coexpression cluster:C3565: Difference between revisions

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{{Coexpression_clusters
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compound catabolic process!0.00153064978927681!7263$GO:0008670!2,4-dienoyl-CoA reductase (NADPH) activity!0.00153064978927681!26063$GO:0009439!cyanate metabolic process!0.00153064978927681!7263$GO:0009440!cyanate catabolic process!0.00153064978927681!7263$GO:0004792!thiosulfate sulfurtransferase activity!0.00244896756971318!7263$GO:0016783!sulfurtransferase activity!0.00306111934572935!7263$GO:0016628!oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor!0.00699581431695691!26063$GO:0008272!sulfate transport!0.0103280842914814!7263$GO:0016782!transferase activity, transferring sulfur-containing groups!0.0210703285937496!7263$GO:0016627!oxidoreductase activity, acting on the CH-CH group of donors!0.0235144913412218!26063$GO:0044270!nitrogen compound catabolic process!0.0235144913412218!7263$GO:0042579!microbody!0.0235144913412218!26063$GO:0005777!peroxisome!0.0235144913412218!26063$GO:0006730!one-carbon compound metabolic process!0.0338166342370627!7263$GO:0031980!mitochondrial lumen!0.03492033499473!7263$GO:0005759!mitochondrial matrix!0.03492033499473!7263$GO:0015698!inorganic anion transport!0.0466420815271067!7263$GO:0044444!cytoplasmic part!0.0480182555675481!26063;7263$GO:0005743!mitochondrial inner membrane!0.0480182555675481!7263$GO:0006820!anion transport!0.0480182555675481!7263$GO:0019866!organelle inner 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|full_id=C3565_Hepatocyte_Mesenchymal_liver_Adipocyte_colon_Alveolar_Renal
|id=C3565
}}

Latest revision as of 12:28, 17 September 2013


Full id: C3565_Hepatocyte_Mesenchymal_liver_Adipocyte_colon_Alveolar_Renal



Phase1 CAGE Peaks

Hg19::chr16:451853..451917,+p1@DECR2
Hg19::chr16:451923..451951,+p2@DECR2
Hg19::chr22:37415475..37415495,-p1@TST


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:0019754one-carbon compound catabolic process0.00153064978927681
GO:00086702,4-dienoyl-CoA reductase (NADPH) activity0.00153064978927681
GO:0009439cyanate metabolic process0.00153064978927681
GO:0009440cyanate catabolic process0.00153064978927681
GO:0004792thiosulfate sulfurtransferase activity0.00244896756971318
GO:0016783sulfurtransferase activity0.00306111934572935
GO:0016628oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor0.00699581431695691
GO:0008272sulfate transport0.0103280842914814
GO:0016782transferase activity, transferring sulfur-containing groups0.0210703285937496
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0235144913412218
GO:0044270nitrogen compound catabolic process0.0235144913412218
GO:0042579microbody0.0235144913412218
GO:0005777peroxisome0.0235144913412218
GO:0006730one-carbon compound metabolic process0.0338166342370627
GO:0031980mitochondrial lumen0.03492033499473
GO:0005759mitochondrial matrix0.03492033499473
GO:0015698inorganic anion transport0.0466420815271067
GO:0044444cytoplasmic part0.0480182555675481
GO:0005743mitochondrial inner membrane0.0480182555675481
GO:0006820anion transport0.0480182555675481
GO:0019866organelle inner membrane0.0480182555675481



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>

Uber Anatomy
Ontology termp-valuen
mesenchyme2.06e-17160
entire embryonic mesenchyme2.06e-17160
trunk1.64e-16199
epithelial tube5.66e-16117
organism subdivision4.86e-15264
unilaminar epithelium8.59e-15148
trunk mesenchyme1.88e-14122
multi-tissue structure1.65e-13342
epithelial vesicle1.04e-1278
anatomical cluster3.35e-12373
epithelium1.81e-11306
vasculature4.42e-1178
vascular system4.42e-1178
cell layer4.43e-11309
multilaminar epithelium6.32e-1183
subdivision of trunk4.11e-10112
muscle tissue5.31e-1064
musculature5.31e-1064
musculature of body5.31e-1064
somite7.91e-1071
presomitic mesoderm7.91e-1071
presumptive segmental plate7.91e-1071
dermomyotome7.91e-1071
trunk paraxial mesoderm7.91e-1071
skeletal muscle tissue8.07e-1062
striated muscle tissue8.07e-1062
myotome8.07e-1062
paraxial mesoderm1.22e-0972
presumptive paraxial mesoderm1.22e-0972
vessel1.46e-0968
dense mesenchyme tissue1.94e-0973
splanchnic layer of lateral plate mesoderm7.48e-0983
endoderm-derived structure9.80e-09160
endoderm9.80e-09160
presumptive endoderm9.80e-09160
epithelial tube open at both ends1.37e-0859
blood vessel1.37e-0859
blood vasculature1.37e-0859
vascular cord1.37e-0859
abdominal segment of trunk8.80e-0860
abdomen8.80e-0860
subdivision of digestive tract9.24e-08118
digestive system1.57e-07145
digestive tract1.57e-07145
primitive gut1.57e-07145
multi-cellular organism3.00e-07656
circulatory system3.86e-07112
trunk region element4.54e-07101
anatomical conduit5.08e-07240
cardiovascular system5.49e-07109
abdomen element8.80e-0754
abdominal segment element8.80e-0754


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)
MA0003.13.8806
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.12.75836
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.15.67475
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.13.97071
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.11.37817
MA0146.18.04252
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.26.2923
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.15.63764
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.27.52072
MA0102.21.88331
MA0258.11.29138
MA0259.10.575594
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
CCNT2#90536.336201576962630.003930750035764890.0189749758717471
ELF1#199734.258097958807540.01295179875054610.0461411143985634
HMGN3#932438.178547723350590.001827766942164210.0108583704023145
JUND#372736.994663941871030.002921845042734990.0156513604358722
NFKB1#479035.488063424193840.006049381815655430.0269271358072385
SIN3A#2594235.408884726815140.006318961977991520.027618584223455
THAP1#55145220.91276306856750.002983447413736940.0158649829146269
YY1#752834.911170749853860.008441455341808260.0328789868890547
ZBTB7A#5134137.35190930787590.002516255860282270.0139955927886254



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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