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{{Coexpression_clusters
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|full_id=C4610_amniotic_immature_cervical_chorionic_Gingival_nasal_epidermoid
|id=C4610
|ontology_enrichment_celltype=CL:0000066!2.31e-21!254;CL:0002076!1.39e-18!43;CL:0000223!1.54e-13!59;CL:0002368!1.25e-09!13;CL:0002251!3.46e-09!21;CL:0000076!2.34e-08!62;CL:0000220!9.61e-08!246;CL:0002321!1.73e-07!248
|ontology_enrichment_disease=DOID:2394!1.55e-10!14;DOID:193!3.74e-09!29;DOID:1749!4.67e-09!14;DOID:120!2.08e-08!27;DOID:305!3.68e-08!106
|ontology_enrichment_uberon=UBERON:0003100!4.08e-14!41;UBERON:0004119!1.01e-13!169;UBERON:0000925!1.01e-13!169;UBERON:0006595!1.01e-13!169;UBERON:0005156!2.75e-13!59;UBERON:0000990!2.75e-13!59;UBERON:0003134!1.53e-12!37;UBERON:0000474!1.53e-12!37;UBERON:0005631!6.16e-11!14;UBERON:0000158!6.16e-11!14;UBERON:0003133!2.96e-10!48;UBERON:0000161!3.84e-09!35;UBERON:0001007!4.41e-09!155;UBERON:0001555!4.41e-09!155;UBERON:0007026!4.41e-09!155;UBERON:0000077!9.19e-09!130;UBERON:0004921!1.83e-08!129;UBERON:0004185!1.83e-08!129;UBERON:0005911!2.14e-08!82;UBERON:0001004!8.44e-08!72;UBERON:0000992!9.57e-08!13;UBERON:0003124!1.46e-07!7;UBERON:0000466!5.42e-07!126;UBERON:0000464!5.62e-07!104;UBERON:0005153!8.18e-07!37;UBERON:0000065!9.95e-07!53
}}

Latest revision as of 14:16, 17 September 2013


Full id: C4610_amniotic_immature_cervical_chorionic_Gingival_nasal_epidermoid



Phase1 CAGE Peaks

Hg19::chr6:47666275..47666296,+p3@GPR115
Hg19::chr6:47666310..47666332,+p1@GPR115
Hg19::chr6:47666342..47666355,+p4@GPR115


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 cell2.21e-22253
endo-epithelial cell1.21e-1942
endodermal cell7.66e-1558
epithelial cell of alimentary canal7.27e-1120
extraembryonic cell1.37e-0819
respiratory epithelial cell1.70e-0813
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane3.97e-1314
membranous layer3.97e-1314
endoderm-derived structure9.39e-13160
endoderm9.39e-13160
presumptive endoderm9.39e-13160
reproductive structure3.57e-1159
reproductive system3.57e-1159
female organism5.95e-1141
female reproductive organ1.04e-1037
female reproductive system1.04e-1037
chorion5.16e-107
orifice1.06e-0836
reproductive organ2.33e-0848
urinary system structure3.29e-0847
organ component layer5.16e-0866
digestive system6.52e-08145
digestive tract6.52e-08145
primitive gut6.52e-08145
renal system6.62e-0848
endo-epithelium9.61e-0882
female gonad1.85e-0713
extraembryonic structure2.66e-0724
mucosa3.35e-0720
Disease
Ontology termp-valuen
ovarian cancer5.62e-1214
squamous cell carcinoma2.15e-1014
carcinoma3.99e-10106
reproductive organ cancer3.66e-0929
female reproductive organ cancer5.13e-0927
cancer4.74e-07235
disease of cellular proliferation5.27e-07239
cell type cancer9.11e-07143


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)
MA0003.10.0471418
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
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
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
MA0139.10.440097
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
MA0035.22.07011
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
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
MA0099.22.08754
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
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
CEBPB#105137.971147625824820.001974187055288560.0115741619999597
EP300#203336.77394172622320.003216880500103790.0168312099869916
FOS#235338.99795530889440.001372499272417130.00901468156166106
GTF2F1#2962312.73966087675770.0004835525047438590.0043584827861348
JUN#3725312.51282919233630.0005103313992726250.00446236612597402
JUND#372736.994663941871030.002921845042734990.0157604882976035
MYC#460935.22228187160940.007020843755740150.0295880034301407
NR3C1#2908314.9730233311730.0002978331194675480.0031006173409162
STAT3#6774310.51946499715420.0008589184530415310.0064531029650532
TRIM28#10155318.59052504526250.0001555969297255280.00198006430408241
USF1#739136.361499277207960.00388404057290560.0191071744415303
USF2#7392312.99219738506960.0004558979393427810.00422893017914741



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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