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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.320160888887285

Latest revision as of 14:17, 17 September 2013


Full id: C4680_Smooth_clear_gastric_Mesothelial_glioma_rectum_melanoma



Phase1 CAGE Peaks

Hg19::chr7:27183263..27183284,-p2@HOXA5
Hg19::chr7:27183291..27183324,-p1@HOXA5
Hg19::chr7:27183325..27183338,-p5@HOXA5


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><br>

Uber Anatomy
Ontology termp-valuen
subdivision of trunk4.38e-19112
trunk2.15e-14199
cavitated compound organ2.17e-1331
epithelial tube1.53e-12117
kidney1.01e-1126
kidney mesenchyme1.01e-1126
upper urinary tract1.01e-1126
kidney rudiment1.01e-1126
kidney field1.01e-1126
abdominal segment of trunk1.26e-1160
abdomen1.26e-1160
trunk region element2.56e-10101
excretory tube6.36e-1016
kidney epithelium6.36e-1016
abdomen element2.07e-0954
abdominal segment element2.07e-0954
mesenchyme3.46e-09160
entire embryonic mesenchyme3.46e-09160
nephron epithelium3.87e-0915
renal tubule3.87e-0915
nephron tubule3.87e-0915
nephron3.87e-0915
uriniferous tubule3.87e-0915
nephrogenic mesenchyme3.87e-0915
renal system5.11e-0948
urinary system structure9.51e-0947
simple squamous epithelium1.53e-0822
blood vessel endothelium1.55e-0818
endothelium1.55e-0818
cardiovascular system endothelium1.55e-0818
epithelial tube open at both ends1.63e-0859
blood vessel1.63e-0859
blood vasculature1.63e-0859
vascular cord1.63e-0859
thoracic segment of trunk3.69e-0852
nephron tubule epithelium6.68e-0810
vessel9.43e-0868
compound organ1.13e-0768
cortex of kidney2.88e-0712
renal parenchyma2.88e-0712
organism subdivision3.61e-07264
squamous epithelium9.64e-0725


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)
MA0003.10.708947
MA0004.13.20493
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.14.13609
MA0059.12.854
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
MA0083.18.72191
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
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
MA0139.16.29415
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
MA0112.20.264678
MA0065.20.277623
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
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285782876353647
CEBPB#105137.971147625824820.001974187055288560.0115806628772906
CTCF#1066435.360256373075030.0064925092527670.028127563523032
EP300#203336.77394172622320.003216880500103790.0168472461413268
MAX#414936.452555509007120.003721913834265510.0187394763986335
MXI1#460139.96157162875930.001011470541259020.00723293199990079
MYC#460935.22228187160940.007020843755740150.0296035326822135
RAD21#5885310.35503389545630.0009004912073565420.00668512945728674
RXRA#6256320.07461713913330.0001235730348432220.00165991565093136
SMC3#9126315.04493284493280.0002935825420371870.00310779111167867
SRF#6722313.79717826216780.0003806615025800190.00376405100056378
STAT3#6774310.51946499715420.0008589184530415310.00645542489329335
USF1#739136.361499277207960.00388404057290560.0191170796641542
USF2#7392312.99219738506960.0004558979393427810.00423193715109952



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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