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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 14:17, 17 September 2013


Full id: C4696_serous_colon_small_MCF7_thyroid_endometrial_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr7:73183842..73183858,-p@chr7:73183842..73183858
-
Hg19::chr7:73184529..73184547,-p2@CLDN3
Hg19::chr7:73184588..73184611,-p1@CLDN3


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 cell2.28e-13253
kidney tubule cell1.56e-1110
nephron tubule epithelial cell1.56e-1110
kidney cell3.02e-0817
kidney epithelial cell3.02e-0817
epithelial cell of nephron3.08e-0815
germ line cell3.89e-077
germ cell3.89e-077
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract2.53e-18118
digestive system1.42e-16145
digestive tract1.42e-16145
primitive gut1.42e-16145
endoderm-derived structure1.90e-14160
endoderm1.90e-14160
presumptive endoderm1.90e-14160
trunk region element2.44e-14101
immaterial anatomical entity7.66e-13117
subdivision of trunk7.92e-13112
foregut8.98e-1287
nephron tubule epithelium1.56e-1110
adult organism1.92e-11114
kidney7.34e-1126
kidney mesenchyme7.34e-1126
upper urinary tract7.34e-1126
kidney rudiment7.34e-1126
kidney field7.34e-1126
endo-epithelium1.32e-1082
abdomen element2.39e-1054
abdominal segment element2.39e-1054
anatomical space4.18e-1095
organ system subdivision2.45e-09223
cavitated compound organ3.83e-0931
excretory tube4.18e-0916
kidney epithelium4.18e-0916
abdominal segment of trunk1.88e-0860
abdomen1.88e-0860
renal system2.11e-0848
gastrointestinal system2.72e-0825
male reproductive organ2.78e-0811
nephron epithelium3.08e-0815
renal tubule3.08e-0815
nephron tubule3.08e-0815
nephron3.08e-0815
uriniferous tubule3.08e-0815
nephrogenic mesenchyme3.08e-0815
intestine4.34e-0817
reproductive structure5.69e-0859
reproductive system5.69e-0859
urinary system structure6.31e-0847
reproductive organ7.89e-0848
lung1.32e-0722
respiratory tube1.32e-0722
respiration organ1.32e-0722
pair of lungs1.32e-0722
lung primordium1.32e-0722
lung bud1.32e-0722
anatomical cluster1.84e-07373
multi-tissue structure2.88e-07342
organ3.14e-07503
primordium8.13e-07160
epithelial bud8.28e-0737
Disease
Ontology termp-valuen
carcinoma3.99e-29106
cell type cancer3.46e-21143
adenocarcinoma2.49e-1525
cancer5.60e-09235
disease of cellular proliferation2.21e-08239
gastrointestinal system cancer7.51e-0814
respiratory system cancer2.29e-0716


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
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
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0113.11.00436
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
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
NANOG#79923219.49651898734180.003427255648501020.0174612982425386



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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