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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.26439946850328

Latest revision as of 12:02, 17 September 2013


Full id: C2304_malignant_mesothelioma_Keratinocyte_Mesenchymal_oral_epidermoid_Mammary



Phase1 CAGE Peaks

Hg19::chr14:59830347..59830363,+p@chr14:59830347..59830363
+
Hg19::chr14:59830369..59830387,+p@chr14:59830369..59830387
+
Hg19::chr14:59830398..59830424,+p@chr14:59830398..59830424
+
Hg19::chr14:59830427..59830451,+p@chr14:59830427..59830451
+


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 cell1.01e-21253
squamous epithelial cell5.72e-1863
embryonic cell3.40e-16250
mesodermal cell1.29e-10121
endo-epithelial cell2.87e-0942
cardiocyte7.56e-0816
endodermal cell2.66e-0758
vascular associated smooth muscle cell9.15e-0732
Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm1.55e-1783
epithelial tube3.73e-12117
epithelial tube open at both ends4.61e-1259
blood vessel4.61e-1259
blood vasculature4.61e-1259
vascular cord4.61e-1259
vasculature1.58e-1178
vascular system1.58e-1178
vessel4.46e-1168
primordium1.82e-10160
circulatory system2.23e-10112
unilaminar epithelium2.24e-10148
artery2.63e-1042
arterial blood vessel2.63e-1042
arterial system2.63e-1042
cardiovascular system4.77e-10109
epithelium4.99e-10306
cell layer7.45e-10309
organism subdivision2.25e-09264
primary circulatory organ3.09e-0927
heart4.12e-0924
primitive heart tube4.12e-0924
primary heart field4.12e-0924
anterior lateral plate mesoderm4.12e-0924
heart tube4.12e-0924
heart primordium4.12e-0924
cardiac mesoderm4.12e-0924
cardiogenic plate4.12e-0924
heart rudiment4.12e-0924
multilaminar epithelium7.94e-0983
systemic artery9.85e-0933
systemic arterial system9.85e-0933
trunk2.13e-08199
anatomical cluster1.10e-07373
anatomical conduit1.14e-07240
aorta6.24e-0721
aortic system6.24e-0721
embryonic structure7.68e-07564
Disease
Ontology termp-valuen
squamous cell carcinoma9.67e-0814
carcinoma6.51e-07106


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.12.44319
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.11.83481
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#105147.971147625824820.0002476385788090830.00267734218760267
EGR1#195844.988179094810140.001615011500076050.0101333845633189
EP300#203346.77394172622320.0004748459821442640.0043372782516324
ESR1#2099430.76860329615451.11467714392546e-064.59596392555984e-05
FOS#235348.99795530889440.0001525147711168630.00194629645413906
GATA2#2624412.7449317335543.78864877853583e-050.000720602239631222
NR3C1#2908414.9730233311731.98868032687801e-050.000442094049933615
TAF1#687243.343046285745290.008005664898701650.0321627802875635
TBP#690843.706770687096390.005296377814784350.0243752876480969



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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