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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.188938360773272

Latest revision as of 11:49, 17 September 2013


Full id: C1655_large_mesothelioma_Fibroblast_giant_oral_mesenchymal_mucinous



Phase1 CAGE Peaks

Hg19::chr12:104674502..104674520,-p5@ENST00000549807
Hg19::chr12:104674521..104674536,-p4@ENST00000549807
Hg19::chr12:104674543..104674573,-p2@ENST00000549807
Hg19::chr12:104674575..104674595,-p3@ENST00000549807
Hg19::chr12:104674604..104674628,-p1@ENST00000549807


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
mesothelial cell6.03e-1619
mesodermal cell7.37e-16121
squamous epithelial cell8.68e-1563
animal cell9.36e-14679
eukaryotic cell9.36e-14679
lining cell2.96e-1358
barrier cell2.96e-1358
epithelial cell1.37e-10253
embryonic cell3.39e-10250
fibroblast4.24e-1076
native cell2.40e-09722
Uber Anatomy
Ontology termp-valuen
vasculature2.15e-0978
vascular system2.15e-0978
vessel6.72e-0968
splanchnic layer of lateral plate mesoderm6.13e-0883
epithelial tube open at both ends9.66e-0859
blood vessel9.66e-0859
blood vasculature9.66e-0859
vascular cord9.66e-0859
epithelial tube1.26e-07117
aorta1.55e-0721
aortic system1.55e-0721
cardiovascular system1.58e-07109
artery1.99e-0742
arterial blood vessel1.99e-0742
arterial system1.99e-0742
unilaminar epithelium2.28e-07148
circulatory system5.34e-07112
larynx7.33e-079
systemic artery9.97e-0733
systemic arterial system9.97e-0733
Disease
Ontology termp-valuen
disease of cellular proliferation3.86e-09239
cancer1.05e-07235
carcinoma2.65e-07106
cell type cancer8.45e-07143


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.15.45153
MA0041.13.838
MA0042.11.48719
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.14.71236
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.15.38057
MA0141.10.520334
MA0142.10.912455
MA0143.11.87149
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.11.35623
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.22.8068
MA0079.23.83292e-05
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CEBPB#105157.971147625824823.10621793420244e-050.00062833680966525
EP300#203356.77394172622327.00901578206049e-050.00110693270718678
FOS#235358.99795530889441.69470025615156e-050.000388738853617863
GATA2#2624512.7449317335542.9719152914525e-060.000101102234893814
JUN#3725512.51282919233633.25800591331781e-060.00010902367176578
JUND#372756.994663941871035.97069468343598e-050.00098324405872496
RFX5#5993512.04791082719513.93714721313598e-060.00012742228626982
STAT3#6774510.51946499715427.759040745861e-060.000220202841428526
TBP#690853.706770687096390.001428755106721120.00917867716004474



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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