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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 12:21, 17 September 2013


Full id: C3192_choriocarcinoma_rectal_breast_pancreatic_adenocarcinoma_Alveolar_Renal



Phase1 CAGE Peaks

Hg19::chr11:66139068..66139120,-p2@SLC29A2
Hg19::chr11:66139128..66139152,-p3@SLC29A2
Hg19::chr11:66139160..66139170,-p9@SLC29A2


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 cell7.14e-33253
endo-epithelial cell3.82e-1742
endodermal cell1.31e-1258
epithelial cell of alimentary canal1.37e-0820
respiratory epithelial cell2.10e-0813
germ line cell3.42e-087
germ cell3.42e-087
epithelial cell of lung6.73e-0819
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.52e-18160
endoderm5.52e-18160
presumptive endoderm5.52e-18160
respiratory system9.41e-1774
respiratory tract2.37e-1654
respiratory primordium8.37e-1638
endoderm of foregut8.37e-1638
digestive system4.56e-15145
digestive tract4.56e-15145
primitive gut4.56e-15145
subdivision of digestive tract1.99e-14118
segment of respiratory tract3.79e-1347
foregut4.20e-1287
epithelial bud4.49e-1137
thoracic cavity element1.26e-0934
thoracic cavity1.26e-0934
anatomical space2.04e-0995
epithelial fold2.56e-0947
thoracic segment organ4.04e-0935
lung6.08e-0922
respiratory tube6.08e-0922
respiration organ6.08e-0922
pair of lungs6.08e-0922
lung primordium6.08e-0922
lung bud6.08e-0922
trunk region element7.56e-09101
organ segment1.00e-0898
endo-epithelium1.25e-0882
respiratory tract epithelium6.73e-0819
lung epithelium6.73e-0819
organ part1.38e-07218
thoracic segment of trunk2.98e-0752
larynx3.97e-079
respiratory system epithelium4.66e-0728
Disease
Ontology termp-valuen
carcinoma8.66e-39106
cell type cancer1.70e-34143
cancer9.11e-23235
disease of cellular proliferation1.81e-21239
adenocarcinoma3.36e-1325
squamous cell carcinoma9.27e-1014
germ cell and embryonal cancer2.61e-0822
germ cell cancer2.61e-0822


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)
MA0003.14.57391
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
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
MA0048.11.62115
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
MA0073.11.36698
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
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0145.11.37817
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.27.95144
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.97249
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.8725
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
CCNT2#90536.336201576962630.003930750035764890.0189259878744756
E2F1#186934.907389214879320.008460985347239390.0323826168528413
EGR1#195834.988179094810140.008056488137383440.0319236470228095
ELK4#2005316.2356816584680.0002336043955745990.00255069623308056
ESR1#2099220.51240219743630.003099741577095180.0163024428729098
HMGN3#932438.178547723350590.001827766942164210.0108374106774548
IRF1#365937.63716375356390.002244692747297240.0127673165142673
MAX#414936.452555509007120.003721913834265510.0185853673888049
MXI1#460139.96157162875930.001011470541259020.00718472229195069
SIN3A#2594235.408884726815140.006318961977991520.0275563100763897
SMARCC2#6601394.15537442689761.19621075407887e-064.8460455758434e-05
SP1#666735.69838137814090.005403962701712170.0245555369215157
TFAP2A#7020316.5186343730450.0002218033880766340.00247435633917278
TFAP2C#7022310.80922860986020.0007916746575753130.00613183844278464
YY1#752834.911170749853860.008441455341808260.0328116846344528
ZBTB7A#5134137.35190930787590.002516255860282270.0139673263774658
ZEB1#6935316.88843201754390.0002075486917327580.00242083737054696



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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