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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 14:16, 17 September 2013


Full id: C4636_squamous_oral_Hep2_epidermoid_mesothelioma_mucinous_ductal



Phase1 CAGE Peaks

Hg19::chr7:101917447..101917479,+p4@CUX1
Hg19::chr7:101917482..101917507,+p6@CUX1
Hg19::chr7:101917509..101917520,+p9@CUX1


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 cell5.50e-36253
squamous epithelial cell3.91e-1263
mesothelial cell1.56e-1119
endodermal cell3.95e-0958
epithelial cell of lung5.07e-0819
Uber Anatomy
Ontology termp-valuen
larynx3.50e-219
digestive system1.51e-18145
digestive tract1.51e-18145
primitive gut1.51e-18145
subdivision of digestive tract3.86e-18118
endoderm-derived structure1.82e-17160
endoderm1.82e-17160
presumptive endoderm1.82e-17160
respiratory primordium2.48e-1738
endoderm of foregut2.48e-1738
segment of respiratory tract1.61e-1447
respiratory tract1.77e-1454
foregut8.62e-1487
endo-epithelium2.19e-1182
respiratory system4.86e-1174
upper respiratory tract6.90e-1119
organ segment4.05e-0998
primordium1.30e-08160
respiratory tract epithelium5.07e-0819
lung epithelium5.07e-0819
organ system subdivision4.03e-07223
epithelial bud8.88e-0737
Disease
Ontology termp-valuen
carcinoma1.83e-51106
cell type cancer9.73e-42143
disease of cellular proliferation1.46e-32239
cancer2.11e-31235
squamous cell carcinoma1.24e-2014
disease of anatomical entity7.50e-1039
adenocarcinoma1.99e-0925
lung cancer1.46e-0815
respiratory system cancer6.30e-0816


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
MA0004.14.60201
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.12.76432
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
MA0058.18.47688
MA0059.11.70014
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
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.12.86846
MA0078.12.37746
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
MA0093.16.48183
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.13.08252
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
MA0143.12.29531
MA0144.11.31729
MA0145.10.273764
MA0146.11.16674
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.21.34467
MA0065.21.39232
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
MA0159.14.68786
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
ATF3#467322.46317452600878.81932387510763e-050.00130004427126657
CEBPB#105137.971147625824820.001974187055288560.0115767614748614
E2F6#187635.017155731697390.00791769806886330.0324166556358154
EGR1#195834.988179094810140.008056488137383440.0322355208252314
EP300#203336.77394172622320.003216880500103790.0168371144908459
FOSL1#8061339.7135797163731.59554825631833e-050.000372540720638565
FOSL2#2355316.93020060456170.0002060162053171620.00244057695861151
HNF4A#3172323.13229036295378.07584663437677e-050.00123399172881884
JUND#372736.994663941871030.002921845042734990.0157629306481843
MAX#414936.452555509007120.003721913834265510.0187340574937036
MXI1#460139.96157162875930.001011470541259020.00723144659491724
MYC#460935.22228187160940.007020843755740150.0295939742909047
NR2C2#7182332.61461090524092.88098172333076e-050.000606260024587833
RXRA#6256320.07461713913330.0001235730348432220.00165970218441246
SP1#666735.69838137814090.005403962701712170.0247830527644191
USF1#739136.361499277207960.00388404057290560.0191089746275527
USF2#7392312.99219738506960.0004558979393427810.00423005729273461
ZNF263#1012738.221841637010680.001799043925565870.011008985090653



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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