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{{Coexpression_clusters
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|full_id=C3583_large_mature_amniotic_heart_renal_Esophageal_breast
|id=C3583
|ontology_enrichment_celltype=CL:0000066!7.15e-13!254;CL:0002076!7.32e-08!43
|ontology_enrichment_disease=DOID:305!9.64e-09!106;DOID:0050687!1.99e-07!143
|ontology_enrichment_uberon=UBERON:0000475!6.22e-21!365;UBERON:0000481!2.49e-19!347;UBERON:0000468!2.92e-18!659;UBERON:0000064!1.93e-17!219;UBERON:0007023!1.42e-15!115;UBERON:0000062!1.55e-15!511;UBERON:0000477!1.40e-14!286;UBERON:0000467!1.99e-14!625;UBERON:0000480!2.62e-14!626;UBERON:0002050!2.89e-13!605;UBERON:0005423!2.89e-13!605;UBERON:0000922!5.37e-13!612;UBERON:0000923!5.42e-13!604;UBERON:0005291!5.42e-13!604;UBERON:0006598!5.42e-13!604;UBERON:0002532!5.42e-13!604;UBERON:0004111!6.66e-13!241;UBERON:0004121!1.02e-11!169;UBERON:0000483!1.79e-11!309;UBERON:0001004!2.37e-11!72;UBERON:0000924!3.85e-11!173;UBERON:0006601!3.85e-11!173;UBERON:0000119!9.32e-11!312;UBERON:0000033!1.61e-10!123;UBERON:0004119!2.16e-10!169;UBERON:0000925!2.16e-10!169;UBERON:0006595!2.16e-10!169;UBERON:0000025!2.49e-10!194;UBERON:0001049!2.96e-10!57;UBERON:0005068!2.96e-10!57;UBERON:0006241!2.96e-10!57;UBERON:0007135!2.96e-10!57;UBERON:0003104!6.55e-10!238;UBERON:0009142!6.55e-10!238;UBERON:0000153!1.21e-09!129;UBERON:0007811!1.21e-09!129;UBERON:0008947!1.45e-09!38;UBERON:0003258!1.45e-09!38;UBERON:0000065!2.76e-09!53;UBERON:0003075!1.38e-08!86;UBERON:0007284!1.38e-08!86;UBERON:0002100!2.84e-08!216;UBERON:0002616!4.45e-08!59;UBERON:0000955!4.48e-08!69;UBERON:0006238!4.48e-08!69;UBERON:0000077!5.74e-08!130;UBERON:0000072!7.00e-08!46;UBERON:0002346!7.05e-08!90;UBERON:0001007!7.95e-08!155;UBERON:0001555!7.95e-08!155;UBERON:0007026!7.95e-08!155;UBERON:0002780!1.02e-07!41;UBERON:0001890!1.02e-07!41;UBERON:0006240!1.02e-07!41;UBERON:0003080!1.39e-07!42;UBERON:0000915!1.81e-07!52;UBERON:0001041!4.53e-07!98;UBERON:0001737!7.87e-07!9;UBERON:0002020!8.66e-07!34;UBERON:0003528!8.66e-07!34
}}

Latest revision as of 12:29, 17 September 2013


Full id: C3583_large_mature_amniotic_heart_renal_Esophageal_breast



Phase1 CAGE Peaks

Hg19::chr16:67207821..67207836,+p5@NOL3
Hg19::chr16:67207838..67207870,+p2@NOL3
Hg19::chr16:67207872..67207900,+p4@NOL3


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 cell1.60e-09253
endo-epithelial cell5.46e-0742
Uber Anatomy
Ontology termp-valuen
adult organism4.05e-17114
multi-tissue structure2.64e-16342
organ part1.02e-15218
organ7.27e-14503
multi-cellular organism2.23e-13656
organ system subdivision4.13e-12223
respiratory system1.09e-1174
anatomical cluster1.61e-11373
endoderm-derived structure2.82e-11160
endoderm2.82e-11160
presumptive endoderm2.82e-11160
anatomical group3.29e-11625
anatomical system3.79e-11624
ectoderm-derived structure4.10e-10171
ectoderm4.10e-10171
presumptive ectoderm4.10e-10171
respiratory primordium5.61e-1038
endoderm of foregut5.61e-1038
respiratory tract7.05e-1054
ecto-epithelium7.90e-10104
anatomical conduit1.55e-09240
neural tube1.91e-0956
neural rod1.91e-0956
future spinal cord1.91e-0956
neural keel1.91e-0956
epithelium3.47e-09306
developing anatomical structure4.21e-09581
embryo5.84e-09592
regional part of nervous system1.32e-0853
regional part of brain1.32e-0853
cell layer1.50e-08309
digestive system2.14e-08145
digestive tract2.14e-08145
primitive gut2.14e-08145
structure with developmental contribution from neural crest2.44e-08132
segment of respiratory tract3.23e-0847
foregut4.02e-0887
organism subdivision4.78e-08264
embryonic structure5.34e-08564
neural plate7.47e-0882
presumptive neural plate7.47e-0882
germ layer1.69e-07560
germ layer / neural crest1.69e-07560
embryonic tissue1.69e-07560
presumptive structure1.69e-07560
germ layer / neural crest derived structure1.69e-07560
epiblast (generic)1.69e-07560
tube2.79e-07192
regional part of forebrain3.62e-0741
forebrain3.62e-0741
anterior neural tube3.62e-0741
future forebrain3.62e-0741
neurectoderm3.70e-0786
brain6.19e-0768
future brain6.19e-0768
larynx6.36e-079
Disease
Ontology termp-valuen
carcinoma2.78e-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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.12.89432
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.13.54511
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
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
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.13.02823
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
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
MYC#460935.22228187160940.007020843755740150.0294052735404935
NR3C1#2908314.9730233311730.0002978331194675480.00308554639064292
SUZ12#23512233.41052060737530.00117826764536030.00799747154180698
ZNF263#1012738.221841637010680.001799043925565870.0109270339367359



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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