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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:29, 17 September 2013


Full id: C3586_serous_breast_choriocarcinoma_pancreatic_malignant_Prostate_maxillary



Phase1 CAGE Peaks

Hg19::chr16:68771187..68771201,+p1@CDH1
Hg19::chr5:68711023..68711075,+p2@MARVELD2
Hg19::chr5:68711076..68711103,+p3@MARVELD2


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:0030054cell junction0.00429571419202788
GO:0044459plasma membrane part0.0299164706866183
GO:0005923tight junction0.0299164706866183
GO:0043296apical junction complex0.0299164706866183
GO:0016327apicolateral plasma membrane0.0299164706866183
GO:0050954sensory perception of mechanical stimulus0.0299164706866183
GO:0007605sensory perception of sound0.0299164706866183
GO:0005911intercellular junction0.0340594182494116
GO:0007156homophilic cell adhesion0.0340594182494116
GO:0005886plasma membrane0.0340594182494116
GO:0016337cell-cell adhesion0.0498875417599653



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 cell2.60e-33253
endodermal cell4.22e-2458
endo-epithelial cell2.12e-2042
epithelial cell of alimentary canal7.60e-1120
respiratory epithelial cell4.96e-0913
epithelial cell of lung2.50e-0719
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.86e-28160
endoderm1.86e-28160
presumptive endoderm1.86e-28160
digestive system7.84e-23145
digestive tract7.84e-23145
primitive gut7.84e-23145
subdivision of digestive tract2.31e-21118
endo-epithelium1.19e-1782
trunk region element2.18e-16101
immaterial anatomical entity2.20e-16117
foregut4.25e-1487
anatomical space1.87e-1295
subdivision of trunk2.68e-12112
respiratory system5.90e-1274
epithelial bud1.87e-1137
renal system3.39e-1148
urinary system structure7.86e-1147
gland2.45e-1059
thoracic cavity element7.74e-1034
thoracic cavity7.74e-1034
thoracic segment organ2.47e-0935
organism subdivision4.88e-09264
epithelial fold6.43e-0947
organ9.58e-09503
exocrine gland9.66e-0931
exocrine system9.66e-0931
lung9.80e-0922
respiratory tube9.80e-0922
respiration organ9.80e-0922
pair of lungs9.80e-0922
lung primordium9.80e-0922
lung bud9.80e-0922
gut epithelium1.38e-0854
respiratory tract1.73e-0854
orifice3.01e-0836
reproductive structure8.01e-0859
reproductive system8.01e-0859
abdomen element1.31e-0754
abdominal segment element1.31e-0754
organ system subdivision1.35e-07223
respiratory system epithelium1.53e-0728
thoracic segment of trunk2.33e-0752
respiratory tract epithelium2.50e-0719
lung epithelium2.50e-0719
extraembryonic membrane3.68e-0714
membranous layer3.68e-0714
reproductive organ8.52e-0748
Disease
Ontology termp-valuen
carcinoma9.70e-26106
cell type cancer6.87e-17143
squamous cell carcinoma4.76e-1214
adenocarcinoma6.34e-0925


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)
MA0003.13.22681
MA0004.11.93041
MA0006.10.639288
MA0007.13.13838
MA0009.11.3275
MA0014.10.758317
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.14.13609
MA0059.12.854
MA0060.11.23283
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
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.846801
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.752137
MA0146.11.70974
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.24.75888
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
MA0102.21.88331
MA0258.11.29138
MA0259.11.40979
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
ATF3#467214.97544968400580.005768294540793880.0259535978608466
MYC#460935.22228187160940.007020843755740150.0294064528175555
SMARCB1#6598212.16847718743830.008675002221921740.0329805451951252
SMC3#9126210.02995522995520.0126656379767470.0457331822933716
TAF7#6879311.43306940492390.0006690181981945830.00541934317856543
USF1#739136.361499277207960.00388404057290560.0190015604924905
USF2#7392312.99219738506960.0004558979393427810.00421246791887293
ZEB1#6935316.88843201754390.0002075486917327580.00242489963260739



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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