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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:16, 17 September 2013


Full id: C296_gall_small_mesothelioma_acute_bronchioalveolar_epidermoid_mixed



Phase1 CAGE Peaks

Hg19::chr10:103952998..103953003,-p@chr10:103952998..103953003
-
Hg19::chr10:124050589..124050596,+p15@BTBD16
Hg19::chr10:73818867..73818877,-p@chr10:73818867..73818877
-
Hg19::chr11:63331619..63331629,-p7@AK025029
Hg19::chr11:86501675..86501685,+p29@PRSS23
Hg19::chr11:86501763..86501768,+p33@PRSS23
Hg19::chr14:68633950..68633964,-p@chr14:68633950..68633964
-
Hg19::chr14:94582961..94582978,+p@chr14:94582961..94582978
+
Hg19::chr17:5813133..5813142,-p@chr17:5813133..5813142
-
Hg19::chr1:27992626..27992630,-p@chr1:27992626..27992630
-
Hg19::chr1:27992654..27992665,-p@chr1:27992654..27992665
-
Hg19::chr1:27992698..27992702,-p@chr1:27992698..27992702
-
Hg19::chr1:27992756..27992763,-p@chr1:27992756..27992763
-
Hg19::chr1:27992774..27992780,-p@chr1:27992774..27992780
-
Hg19::chr1:79107935..79107976,+p@chr1:79107935..79107976
+
Hg19::chr1:94583454..94583465,-p@chr1:94583454..94583465
-
Hg19::chr20:4100484..4100497,+p1@BC027448
Hg19::chr20:4100520..4100530,+p2@BC027448
Hg19::chr20:4100562..4100570,+p4@BC027448
Hg19::chr20:4100596..4100603,+p5@BC027448
Hg19::chr21:42613665..42613680,+p10@BACE2
Hg19::chr22:31985409..31985436,+p@chr22:31985409..31985436
+
Hg19::chr22:31985448..31985465,+p@chr22:31985448..31985465
+
Hg19::chr22:50983547..50983560,-p@chr22:50983547..50983560
-
Hg19::chr2:121003683..121003689,-p@chr2:121003683..121003689
-
Hg19::chr2:42157172..42157179,-p@chr2:42157172..42157179
-
Hg19::chr2:42157397..42157411,-p@chr2:42157397..42157411
-
Hg19::chr3:186648149..186648166,+p12@ST6GAL1
Hg19::chr3:195516631..195516648,-p@chr3:195516631..195516648
-
Hg19::chr3:195516657..195516687,-p@chr3:195516657..195516687
-
Hg19::chr3:23688310..23688316,+p@chr3:23688310..23688316
+
Hg19::chr4:6698835..6698866,+p@chr4:6698835..6698866
+
Hg19::chr5:147644551..147644576,+p@chr5:147644551..147644576
+
Hg19::chr5:147645292..147645302,+p@chr5:147645292..147645302
+
Hg19::chr5:84867331..84867340,-p@chr5:84867331..84867340
-
Hg19::chr5:84943630..84943645,-p@chr5:84943630..84943645
-
Hg19::chr9:95736745..95736757,+p9@FGD3
Hg19::chr9:95736758..95736771,+p7@FGD3
Hg19::chr9:95736796..95736808,+p11@FGD3
Hg19::chr9:95736917..95736936,+p10@FGD3
Hg19::chr9:95737369..95737393,+p18@FGD3
Hg19::chr9:95737958..95737978,+p@chr9:95737958..95737978
+


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

GO IDGO nameFDR corrected p-value
GO:0009101glycoprotein biosynthetic process0.0153040198506013
GO:0009100glycoprotein metabolic process0.0153040198506013
GO:0042985negative regulation of amyloid precursor protein biosynthetic process0.0153040198506013
GO:0042983amyloid precursor protein biosynthetic process0.0153040198506013
GO:0003835beta-galactoside alpha-2,6-sialyltransferase activity0.0153040198506013
GO:0042984regulation of amyloid precursor protein biosynthetic process0.0153040198506013
GO:0009049aspartic-type signal peptidase activity0.0163961987631881
GO:0016486peptide hormone processing0.0187766779372494
GO:0032488Cdc42 protein signal transduction0.0187766779372494
GO:0043088regulation of Cdc42 GTPase activity0.0187766779372494
GO:0032489regulation of Cdc42 protein signal transduction0.0187766779372494
GO:0032319regulation of Rho GTPase activity0.0198846865302194
GO:0033619membrane protein proteolysis0.0198846865302194
GO:0009003signal peptidase activity0.0198846865302194
GO:0006509membrane protein ectodomain proteolysis0.0198846865302194
GO:0042982amyloid precursor protein metabolic process0.0200747034966908
GO:0050435beta-amyloid metabolic process0.0229384663849809
GO:0009311oligosaccharide metabolic process0.0275148176906598
GO:0046847filopodium formation0.0275148176906598
GO:0030035microspike biogenesis0.0275148176906598
GO:0004194pepsin A activity0.0283849614143019
GO:0005794Golgi apparatus0.0284450184777538
GO:0004175endopeptidase activity0.0339601840165598
GO:0008373sialyltransferase activity0.0339601840165598
GO:0030027lamellipodium0.0339601840165598
GO:0022603regulation of anatomical structure morphogenesis0.0339601840165598
GO:0022604regulation of cell morphogenesis0.0339601840165598
GO:0008360regulation of cell shape0.0339601840165598
GO:0001726ruffle0.0339601840165598
GO:0030031cell projection biogenesis0.0381565712327612
GO:0009306protein secretion0.0420779689934136
GO:0030173integral to Golgi membrane0.0436133239286936
GO:0031228intrinsic to Golgi membrane0.0484185353590127
GO:0031252leading edge0.0484185353590127
GO:0006959humoral immune response0.0489862934759819



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>

Cell Type
Ontology termp-valuen
epithelial cell of gall bladder2.74e-502
Uber Anatomy
Ontology termp-valuen
gallbladder4.27e-343
gall bladder primordium4.27e-343
placenta7.14e-264
allantois7.14e-264
chorion1.91e-157
biliary system2.19e-129
biliary tree2.19e-129
biliary bud2.19e-129
extraembryonic membrane2.00e-0814
membranous layer2.00e-0814
viscus7.18e-0718


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)
MA0003.15.38639e-08
MA0004.10.0477118
MA0006.10.151261
MA0007.10.161987
MA0009.10.832604
MA0014.12.98856e-05
MA0017.10.648923
MA0019.10.108546
MA0024.10.234026
MA0025.10.413966
MA0027.11.81465
MA0028.10.0137439
MA0029.10.24734
MA0030.10.23941
MA0031.10.196546
MA0038.10.0872867
MA0040.10.700752
MA0041.10.439865
MA0042.10.167031
MA0043.10.309473
MA0046.10.301098
MA0048.10.210301
MA0050.11.05013
MA0051.11.01479
MA0052.10.254136
MA0055.10.0684641
MA0056.10
MA0057.10.00336561
MA0058.10.0224128
MA0059.10.0963316
MA0060.10.737327
MA0061.10.0074676
MA0063.10
MA0066.10.294839
MA0067.10.570397
MA0068.10.00320233
MA0069.10.298233
MA0070.11.43734
MA0071.11.36116
MA0072.10.286664
MA0073.10.00148799
MA0074.10.602446
MA0076.10.0258596
MA0077.10.281032
MA0078.10.134513
MA0081.10.0964507
MA0083.12.32364
MA0084.10.739331
MA0087.10.284873
MA0088.10.005582
MA0089.10
MA0090.12.68521
MA0091.11.11018
MA0092.10.340194
MA0093.10.0118584
MA0095.10
MA0098.10
MA0100.10.0935814
MA0101.10.0123183
MA0103.10.748564
MA0105.10.0209343
MA0106.10.106627
MA0107.10.00459001
MA0108.20.566954
MA0109.10
MA0111.10.311824
MA0113.10.742167
MA0114.10.494361
MA0115.10.50405
MA0116.10.0827104
MA0117.10.337847
MA0119.10.412667
MA0122.10.941347
MA0124.10.468805
MA0125.11.03242
MA0130.10
MA0131.10.144593
MA0132.10
MA0133.10
MA0135.10.332279
MA0136.10.0904607
MA0139.10.0581541
MA0140.11.35002
MA0141.10.0950609
MA0142.10.52354
MA0143.10.368245
MA0144.10.659119
MA0145.10.0206228
MA0146.10.0288193
MA0147.10.0286031
MA0148.11.68086
MA0149.10.0660182
MA0062.20.000932536
MA0035.21.34707
MA0039.20.00140111
MA0138.20.135185
MA0002.20.087342
MA0137.20.355048
MA0104.20.0121567
MA0047.20.677402
MA0112.20.269149
MA0065.20.441936
MA0150.10.116147
MA0151.10
MA0152.10.539107
MA0153.10.385866
MA0154.10.0436337
MA0155.10.0998378
MA0156.10.183428
MA0157.10.160178
MA0158.10
MA0159.10.0288354
MA0160.10.833151
MA0161.10
MA0162.11.37079e-05
MA0163.10.00265856
MA0164.10.121237
MA0080.20.155147
MA0018.20.348219
MA0099.20.919341
MA0079.22.57234e-13
MA0102.20.773745
MA0258.10.0562541
MA0259.10.0317654
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
BDP1#558144100.014610389618.64489907996505e-085.1328289653921e-06
ESR1#209953.662928963827910.01133587996099810.0415712618858345
POLR3A#11128432.29829619921367.65719882473563e-060.00021820196127055



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

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