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{{Coexpression_clusters
{
|full_id=C4136_small_Intestinal_endometrial_Mesothelial_Fibroblast_Prostate_colon

Latest revision as of 12:40, 17 September 2013


Full id: C4136_small_Intestinal_endometrial_Mesothelial_Fibroblast_Prostate_colon



Phase1 CAGE Peaks

Hg19::chr2:162930503..162930521,-p3@DPP4
Hg19::chr2:162930536..162930551,-p5@DPP4
Hg19::chr2:162930560..162930613,-p1@DPP4


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>

Uber Anatomy
Ontology termp-valuen
mesenchyme1.91e-17160
entire embryonic mesenchyme1.91e-17160
trunk mesenchyme8.60e-16122
muscle tissue4.76e-1464
musculature4.76e-1464
musculature of body4.76e-1464
somite1.10e-1371
presomitic mesoderm1.10e-1371
presumptive segmental plate1.10e-1371
dermomyotome1.10e-1371
trunk paraxial mesoderm1.10e-1371
skeletal muscle tissue1.66e-1362
striated muscle tissue1.66e-1362
myotome1.66e-1362
epithelial tube4.04e-13117
paraxial mesoderm4.75e-1372
presumptive paraxial mesoderm4.75e-1372
unilaminar epithelium7.40e-13148
dense mesenchyme tissue1.94e-1273
trunk6.64e-12199
epithelial vesicle9.77e-1278
splanchnic layer of lateral plate mesoderm1.58e-1183
multilaminar epithelium5.22e-1183
organism subdivision6.65e-09264
mesoderm9.19e-08315
mesoderm-derived structure9.19e-08315
presumptive mesoderm9.19e-08315
cardiovascular system2.44e-07109
heart4.59e-0724
primitive heart tube4.59e-0724
primary heart field4.59e-0724
anterior lateral plate mesoderm4.59e-0724
heart tube4.59e-0724
heart primordium4.59e-0724
cardiac mesoderm4.59e-0724
cardiogenic plate4.59e-0724
heart rudiment4.59e-0724
circulatory system5.09e-07112
artery6.31e-0742
arterial blood vessel6.31e-0742
arterial system6.31e-0742
gut epithelium7.79e-0754
Disease
Ontology termp-valuen
ovarian cancer2.98e-0914
reproductive organ cancer3.24e-0729
female reproductive organ cancer5.77e-0727


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)
MA0003.16.86157
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
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
MA0073.10.0185922
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
MA0105.12.3269
MA0106.10.986396
MA0107.10.556367
MA0108.24.2163
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.15.05652
MA0154.12.30945
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
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
CHD2#1106310.34402283411690.0009033701102746880.00661388509968301
CTCF#1066435.360256373075030.0064925092527670.028005582927876
E2F1#186934.907389214879320.008460985347239390.0326120773796994
EBF1#187938.9064668465690.00141523283560980.00916793835245332
EP300#203336.77394172622320.003216880500103790.0167749042615508
FOXA1#3169311.08141974938550.000734755275698670.00582268049462731
HDAC2#3066313.41562023662630.0004140761399857210.0039200233850588
PAX5#507936.669565531177830.003370290999677260.0173231862648405
TCF7L2#6934310.77017656313730.0008003181298398380.00614953098604641



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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