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{{Coexpression_clusters
{
|full_id=C1550_Osteoblast_Mesothelial_acute_leukemia_Prostate_Fibroblast_Lens

Latest revision as of 11:47, 17 September 2013


Full id: C1550_Osteoblast_Mesothelial_acute_leukemia_Prostate_Fibroblast_Lens



Phase1 CAGE Peaks

Hg19::chr9:21974796..21974810,-p16@CDKN2A
Hg19::chr9:21974820..21974906,-p2@CDKN2A
Hg19::chr9:21975060..21975078,-p4@CDKN2A
Hg19::chr9:21975088..21975104,-p11@CDKN2A
Hg19::chr9:21975118..21975140,-p8@CDKN2A
Hg19::chr9:21975146..21975164,-p5@CDKN2A


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
artery2.27e-2042
arterial blood vessel2.27e-2042
arterial system2.27e-2042
vasculature1.56e-1778
vascular system1.56e-1778
systemic artery1.56e-1633
systemic arterial system1.56e-1633
epithelial tube open at both ends5.17e-1659
blood vessel5.17e-1659
blood vasculature5.17e-1659
vascular cord5.17e-1659
vessel1.03e-1568
splanchnic layer of lateral plate mesoderm6.53e-1383
multilaminar epithelium1.01e-1183
cardiovascular system4.13e-11109
circulatory system1.15e-10112
epithelial vesicle3.09e-1078
somite8.59e-1071
presomitic mesoderm8.59e-1071
presumptive segmental plate8.59e-1071
dermomyotome8.59e-1071
trunk paraxial mesoderm8.59e-1071
dense mesenchyme tissue1.08e-0973
aorta1.74e-0921
aortic system1.74e-0921
paraxial mesoderm2.05e-0972
presumptive paraxial mesoderm2.05e-0972
epithelial tube2.55e-09117
organism subdivision7.26e-09264
skeletal muscle tissue1.91e-0862
striated muscle tissue1.91e-0862
myotome1.91e-0862
epithelium2.93e-08306
cell layer8.36e-08309
muscle tissue9.99e-0864
musculature9.99e-0864
musculature of body9.99e-0864
larynx1.11e-079
unilaminar epithelium1.41e-07148
surface structure3.36e-0799
trunk4.03e-07199


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)
MA0003.13.05245
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.788761
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.12.77054
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.12.30818
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.11.15845
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.19.01711
MA0074.10.660398
MA0076.13.08133
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.11.34409
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.13.11622
MA0145.13.00011
MA0146.10.718193
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.23.52102
MA0035.20.621793
MA0039.20.82735
MA0138.20.765223
MA0002.20.255126
MA0137.21.87543
MA0104.20.735746
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.12.59196
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.978497
MA0163.15.08954
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.23.22572
MA0102.21.58513
MA0258.11.43672
MA0259.10.336472
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
CTBP2#1488662.71700033932811.6349770986689e-111.99247810044202e-09
EBF1#187968.9064668465692.00211291586927e-067.32651264262336e-05
ELK4#2005616.2356816584685.45305335722442e-083.44740580856635e-06
GABPB1#255367.067683836182178.01905956107035e-060.000222917902980736
MXI1#460169.96157162875931.02262624227062e-064.31001057774419e-05
POLR2A#543062.147453176558070.01019570676818780.0380813038825108
SMARCB1#6598618.25271578115742.70039220880305e-081.85665741866479e-06
SP1#666765.69838137814092.91961319085282e-050.000610331229062206
SUZ12#23512433.41052060737532.29902183370319e-068.19479663106236e-05
TAF1#687263.343046285745290.0007162474284635620.00573959680666815
TFAP2A#7020616.5186343730454.91595718330683e-083.16338664366841e-06
TFAP2C#7022610.80922860986026.2644941908553e-072.86955047718744e-05
ZNF263#1012768.221841637010683.23542093046082e-060.000108895947971769



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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