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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:33, 17 September 2013


Full id: C889_mesothelioma_mesodermal_lung_placenta_umbilical_Urothelial_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr12:106477805..106477824,-p13@NUAK1
Hg19::chr12:80175910..80175928,-p31@PPP1R12A
Hg19::chr17:26890530..26890545,-p@chr17:26890530..26890545
-
Hg19::chr17:26890583..26890593,-p@chr17:26890583..26890593
-
Hg19::chr17:67586124..67586131,+p1@uc002jil.2
Hg19::chr3:129023260..129023267,+p3@AF035296
Hg19::chr4:23022304..23022336,+p@chr4:23022304..23022336
+
Hg19::chr8:141728444..141728461,-p23@PTK2
Hg19::chr8:141728472..141728496,-p19@PTK2


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

p.valueFDRnGenesnPathwayName
0.0001458532098643570.02642575022000882200Focal adhesion (KEGG):04510
0.0001669873631596130.02642575022000882214Regulation of actin cytoskeleton (KEGG):04810
0.0001288708350416320.02642575022000882188Focal Adhesion (Wikipathways):WP306
7.66167144514812e-050.02642575022000882145Regulation of Actin Cytoskeleton (Wikipathways):WP51



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

GO IDGO nameFDR corrected p-value
GO:0007172signal complex assembly0.0300359574741371
GO:0042169SH2 domain binding0.0300359574741371
GO:0005925focal adhesion0.0300359574741371
GO:0005924cell-substrate adherens junction0.0300359574741371
GO:0004672protein kinase activity0.0300359574741371
GO:0006937regulation of muscle contraction0.0300359574741371
GO:0006468protein amino acid phosphorylation0.0300359574741371
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0300359574741371
GO:0030055cell-matrix junction0.0300359574741371
GO:0005912adherens junction0.0300359574741371
GO:0016310phosphorylation0.0300359574741371
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0300359574741371
GO:0005856cytoskeleton0.0300359574741371
GO:0043623cellular protein complex assembly0.030700721916763
GO:0016301kinase activity0.030700721916763
GO:0006793phosphorus metabolic process0.030700721916763
GO:0006796phosphate metabolic process0.030700721916763
GO:0016323basolateral plasma membrane0.030700721916763
GO:0007229integrin-mediated signaling pathway0.030700721916763
GO:0016772transferase activity, transferring phosphorus-containing groups0.0369879296170742
GO:0019904protein domain specific binding0.0409697638742895
GO:0043687post-translational protein modification0.0434369027088801
GO:0003012muscle system process0.0465227350691899
GO:0006936muscle contraction0.0465227350691899
GO:0006464protein modification process0.0492255124386033
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0492255124386033
GO:0005515protein binding0.0492255124386033
GO:0005524ATP binding0.0492255124386033
GO:0043412biopolymer modification0.0492255124386033
GO:0032559adenyl ribonucleotide binding0.0492255124386033
GO:0043232intracellular non-membrane-bound organelle0.0492255124386033
GO:0043228non-membrane-bound organelle0.0492255124386033
GO:0030554adenyl nucleotide binding0.0492255124386033



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 cell2.15e-2019
cortical cell of adrenal gland3.71e-092
Uber Anatomy
Ontology termp-valuen
urinary bladder6.94e-092
lower urinary tract6.94e-092
Disease
Ontology termp-valuen
papillary adenocarcinoma1.04e-161


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)
MA0003.10.0149552
MA0004.11.06719
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.0324647
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.11.69202
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.693769
MA0056.10
MA0057.10.253359
MA0058.10.86817
MA0059.10.865474
MA0060.10.488252
MA0061.10.432181
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.931587
MA0091.10.417885
MA0092.10.381858
MA0093.11.35827
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.746654
MA0103.10.257174
MA0105.10.229733
MA0106.10.554855
MA0107.11.11943
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.13.17401
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.0045741
MA0147.10.607251
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0189957
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.486672
MA0047.20.542971
MA0112.20.166662
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.11.20819
MA0153.10.969315
MA0154.10.225151
MA0155.10.0402662
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.000337902
MA0102.21.41188
MA0258.11.01999
MA0259.10.624802
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

No analysis results for this cluster

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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