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{{Coexpression_clusters
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|full_id=C3760_lung_bile_large_papillotubular_keratoacanthoma_oral_endometrial
|id=C3760
|ontology_enrichment_celltype=CL:0000066!3.74e-18!254;CL:0000223!1.84e-15!59;CL:0002076!3.70e-13!43
|ontology_enrichment_disease=DOID:305!3.53e-22!106;DOID:0050687!3.07e-15!143;DOID:299!4.89e-12!25;DOID:1749!8.76e-10!14;DOID:7!3.01e-07!39;DOID:162!9.16e-07!235
|ontology_enrichment_uberon=UBERON:0007023!5.19e-31!115;UBERON:0000062!4.26e-19!511;UBERON:0001049!1.68e-16!57;UBERON:0005068!1.68e-16!57;UBERON:0006241!1.68e-16!57;UBERON:0007135!1.68e-16!57;UBERON:0004119!3.32e-14!169;UBERON:0000925!3.32e-14!169;UBERON:0006595!3.32e-14!169;UBERON:0000955!4.72e-13!69;UBERON:0006238!4.72e-13!69;UBERON:0001017!5.35e-13!82;UBERON:0003080!6.02e-13!42;UBERON:0001007!9.39e-13!155;UBERON:0001555!9.39e-13!155;UBERON:0007026!9.39e-13!155;UBERON:0002780!1.15e-12!41;UBERON:0001890!1.15e-12!41;UBERON:0006240!1.15e-12!41;UBERON:0002616!2.07e-12!59;UBERON:0000033!2.22e-12!123;UBERON:0005743!2.83e-12!86;UBERON:0005177!7.57e-12!107;UBERON:0003075!7.88e-12!86;UBERON:0007284!7.88e-12!86;UBERON:0000475!9.74e-12!365;UBERON:0004921!1.10e-11!129;UBERON:0004185!1.10e-11!129;UBERON:0005911!1.24e-11!82;UBERON:0000153!1.92e-11!129;UBERON:0007811!1.92e-11!129;UBERON:0002020!3.24e-11!34;UBERON:0003528!3.24e-11!34;UBERON:0001893!3.40e-11!34;UBERON:0004111!3.63e-11!241;UBERON:0002050!5.25e-11!605;UBERON:0005423!5.25e-11!605;UBERON:0002791!8.40e-11!33;UBERON:0000923!9.15e-11!604;UBERON:0005291!9.15e-11!604;UBERON:0006598!9.15e-11!604;UBERON:0002532!9.15e-11!604;UBERON:0001041!9.40e-11!98;UBERON:0000467!1.43e-10!625;UBERON:0002346!1.60e-10!90;UBERON:0004121!1.63e-10!169;UBERON:0000480!1.92e-10!626;UBERON:0001869!3.20e-10!32;UBERON:0000077!4.10e-10!130;UBERON:0000922!4.16e-10!612;UBERON:0000073!5.51e-10!94;UBERON:0001016!5.51e-10!94;UBERON:0000924!1.05e-09!173;UBERON:0006601!1.05e-09!173;UBERON:0000481!1.46e-09!347;UBERON:0001004!1.60e-09!72;UBERON:0000468!2.63e-09!659;UBERON:0000466!2.92e-09!126;UBERON:0009569!9.56e-09!113;UBERON:0003056!2.21e-08!61;UBERON:0002619!2.91e-08!22;UBERON:0000025!3.90e-08!194;UBERON:0000477!4.28e-08!286;UBERON:0000064!1.08e-07!219;UBERON:0002365!1.23e-07!31;UBERON:0002330!1.23e-07!31;UBERON:0000483!1.40e-07!309;UBERON:0005157!1.44e-07!51;UBERON:0005153!1.56e-07!37;UBERON:0002530!2.45e-07!59;UBERON:0000065!3.05e-07!53;UBERON:0000119!3.29e-07!312;UBERON:0001950!3.62e-07!20;UBERON:0000956!3.76e-07!25;UBERON:0000203!3.76e-07!25;UBERON:0005178!5.12e-07!34;UBERON:0002224!5.12e-07!34;UBERON:0002048!8.74e-07!22;UBERON:0000117!8.74e-07!22;UBERON:0000171!8.74e-07!22;UBERON:0000170!8.74e-07!22;UBERON:0005597!8.74e-07!22;UBERON:0000118!8.74e-07!22;UBERON:0009497!8.75e-07!25;UBERON:0000015!8.75e-07!25;UBERON:0002423!8.75e-07!25;UBERON:0006235!8.75e-07!25;UBERON:0004161!8.75e-07!25
}}

Latest revision as of 12:32, 17 September 2013


Full id: C3760_lung_bile_large_papillotubular_keratoacanthoma_oral_endometrial



Phase1 CAGE Peaks

Hg19::chr19:16045510..16045553,-p8@CYP4F11
Hg19::chr19:16045619..16045649,-p2@CYP4F11
Hg19::chr19:16045665..16045708,-p1@CYP4F11


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 cell3.01e-15253
endodermal cell4.75e-1458
endo-epithelial cell1.12e-1142
Uber Anatomy
Ontology termp-valuen
adult organism2.43e-28114
organ system subdivision1.34e-19223
neural tube2.72e-1956
neural rod2.72e-1956
future spinal cord2.72e-1956
neural keel2.72e-1956
regional part of nervous system4.02e-1753
regional part of brain4.02e-1753
central nervous system9.94e-1581
regional part of forebrain2.17e-1441
forebrain2.17e-1441
anterior neural tube2.17e-1441
future forebrain2.17e-1441
brain4.71e-1468
future brain4.71e-1468
anatomical conduit8.53e-14240
brain grey matter1.08e-1234
gray matter1.08e-1234
telencephalon1.28e-1234
trunk region element1.98e-12101
endoderm-derived structure5.64e-12160
endoderm5.64e-12160
presumptive endoderm5.64e-12160
nervous system6.63e-1289
foregut1.18e-1187
regional part of telencephalon2.61e-1132
anatomical cluster2.69e-11373
cerebral hemisphere2.97e-1132
organ3.98e-11503
multi-tissue structure4.36e-11342
ecto-epithelium5.31e-11104
tube6.31e-11192
digestive system1.05e-10145
digestive tract1.05e-10145
primitive gut1.05e-10145
neural plate1.12e-1082
presumptive neural plate1.12e-1082
subdivision of digestive tract6.64e-10118
endo-epithelium1.09e-0982
neurectoderm1.23e-0986
regional part of cerebral cortex2.06e-0922
immaterial anatomical entity3.07e-09117
subdivision of trunk1.05e-08112
ectoderm-derived structure1.32e-08171
ectoderm1.32e-08171
presumptive ectoderm1.32e-08171
pre-chordal neural plate3.23e-0861
respiratory system5.88e-0874
neocortex6.17e-0820
cerebral cortex9.32e-0825
pallium9.32e-0825
epithelium1.16e-07306
thoracic cavity element1.73e-0734
thoracic cavity1.73e-0734
developing anatomical structure2.05e-07581
cell layer2.28e-07309
thoracic segment organ4.08e-0735
neural nucleus5.59e-079
nucleus of brain5.59e-079
abdomen element6.07e-0754
abdominal segment element6.07e-0754
epithelial bud6.84e-0737
basal ganglion6.92e-079
nuclear complex of neuraxis6.92e-079
aggregate regional part of brain6.92e-079
collection of basal ganglia6.92e-079
cerebral subcortex6.92e-079
embryo7.20e-07592
Disease
Ontology termp-valuen
carcinoma5.49e-18106
squamous cell carcinoma1.68e-1214
cell type cancer5.26e-12143
adenocarcinoma9.05e-1225


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
MA0028.11.58389
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
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
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.14.04858
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
MA0145.13.85295
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.24.7367
MA0065.20.760954
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.12.7096
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.13.27997
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
ELF1#199734.258097958807540.01295179875054610.0462136286200302



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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