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{{Coexpression_clusters
{
|full_id=C1716_Corneal_oral_Keratinocyte_mesothelioma_Esophageal_Urothelial_anaplastic

Latest revision as of 11:50, 17 September 2013


Full id: C1716_Corneal_oral_Keratinocyte_mesothelioma_Esophageal_Urothelial_anaplastic



Phase1 CAGE Peaks

Hg19::chr14:23451697..23451713,-p4@AJUBA
Hg19::chr14:23451725..23451742,-p1@AJUBA
Hg19::chr14:23451753..23451767,-p2@AJUBA
Hg19::chr14:23451797..23451814,-p3@AJUBA
Hg19::chr14:23451816..23451828,-p5@AJUBA


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 cell2.54e-50253
embryonic cell1.39e-33250
endodermal cell4.37e-1858
endo-epithelial cell2.44e-1642
animal cell5.31e-16679
eukaryotic cell5.31e-16679
squamous epithelial cell1.79e-1563
mesodermal cell7.33e-11121
epithelial cell of alimentary canal5.73e-0920
lining cell1.22e-0858
barrier cell1.22e-0858
respiratory epithelial cell7.13e-0813
kidney cell9.11e-0717
kidney epithelial cell9.11e-0717
Uber Anatomy
Ontology termp-valuen
organism subdivision1.28e-21264
endoderm-derived structure1.61e-18160
endoderm1.61e-18160
presumptive endoderm1.61e-18160
trunk1.21e-14199
digestive system1.85e-13145
digestive tract1.85e-13145
primitive gut1.85e-13145
multi-tissue structure2.66e-13342
mesenchyme9.03e-13160
entire embryonic mesenchyme9.03e-13160
unilaminar epithelium1.73e-12148
anatomical cluster3.91e-12373
surface structure6.73e-1299
cell layer3.29e-11309
endo-epithelium3.45e-1182
epithelium3.53e-11306
urinary system structure3.67e-1147
multi-cellular organism5.47e-11656
renal system7.79e-1148
trunk region element1.50e-10101
subdivision of trunk3.86e-10112
anatomical system3.00e-09624
trunk mesenchyme4.52e-09122
epithelial tube4.72e-09117
anatomical group5.18e-09625
subdivision of digestive tract5.28e-09118
primordium5.29e-09160
gut epithelium9.32e-0954
abdomen element2.51e-0854
abdominal segment element2.51e-0854
head5.33e-0856
abdominal segment of trunk5.65e-0860
abdomen5.65e-0860
subdivision of head8.65e-0849
ectodermal placode1.32e-0731
immaterial anatomical entity1.78e-07117
respiratory system2.05e-0774
foregut2.56e-0787
gland2.71e-0759
exocrine gland5.26e-0731
exocrine system5.26e-0731
anterior region of body8.37e-0762
craniocervical region8.37e-0762
Disease
Ontology termp-valuen
cell type cancer3.11e-12143
carcinoma4.60e-12106
disease of anatomical entity5.11e-0939


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
MA0006.12.97829
MA0007.10.606704
MA0009.11.11255
MA0014.11.02528
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
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.12.36624
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.14.22427
MA0067.11.43651
MA0068.11.28241
MA0069.14.04346
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.12.96921
MA0101.10.459973
MA0103.10.442769
MA0105.11.00065
MA0106.10.779931
MA0107.10.985964
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
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.777733
MA0035.20.691506
MA0039.21.50246
MA0138.20.837782
MA0002.22.29226
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.21.96224
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.26.70786
MA0102.21.66336
MA0258.10.914277
MA0259.12.71109
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#90556.336201576962639.78880505817628e-050.00138979474098814
CHD2#1106510.34402283411698.43981772346334e-060.000230142590919266
CTBP2#1488562.71700033932811.02712351233917e-099.50148383571214e-08
CTCF#1066455.360256373075030.0002259278299937090.00249663280464638
E2F1#186954.907389214879320.0003512818099256460.00352493475661266
E2F6#187655.017155731697390.0003144978599297790.00322650707202418
EGR1#195854.988179094810140.0003237398000590710.00330638186762853
ELF1#199754.258097958807540.0007142416939776840.00572835879875099
HDAC2#3066410.7324961893010.0001450965797478750.00188549728658558
IRF1#365957.63716375356393.84754333311872e-050.000723763649437295
JUND#372756.994663941871035.97069468343598e-050.000983709389562028
MXI1#460159.96157162875931.01894348670516e-050.000266509989501628
MYC#460955.22228187160940.0002573944848850610.00276336581074331
RFX5#5993512.04791082719513.93714721313598e-060.000127461784808651
SMARCB1#6598518.25271578115744.93125075403021e-072.31467369662994e-05
SP1#666755.69838137814090.000166391843712550.00204156458711173
SRF#6722513.79717826216781.9987012616697e-067.31915712017959e-05
TAF1#687253.343046285745290.002394600090870310.0135264015842071
TBP#690853.706770687096390.001428755106721120.00918263105174445
TCF7L2#6934510.77017656313736.89693748574565e-060.000199697603014635
TRIM28#10155518.59052504526254.49912775886781e-072.13583820003816e-05
ZBTB7A#5134157.35190930787594.65425347594289e-050.000815443010860592
ZNF263#1012758.221841637010682.6606316672286e-050.000570816989921299



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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