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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:09, 17 September 2013


Full id: C267_pancreatic_placenta_choriocarcinoma_testicular_teratocarcinoma_chorionic_clear



Phase1 CAGE Peaks

Hg19::chr11:2314912..2314928,-p@chr11:2314912..2314928
-
Hg19::chr12:122107309..122107329,-p6@MORN3
Hg19::chr12:122107501..122107512,-p5@MORN3
Hg19::chr12:122107518..122107540,-p4@MORN3
Hg19::chr12:19556947..19556956,+p14@AEBP2
Hg19::chr12:19556960..19556982,+p10@AEBP2
Hg19::chr12:19556998..19557013,+p6@AEBP2
Hg19::chr12:19571344..19571348,+p@chr12:19571344..19571348
+
Hg19::chr12:68185216..68185218,+p@chr12:68185216..68185218
+
Hg19::chr12:71771004..71771010,+p@chr12:71771004..71771010
+
Hg19::chr12:78959588..78959592,+p@chr12:78959588..78959592
+
Hg19::chr12:79954988..79954992,-p@chr12:79954988..79954992
-
Hg19::chr13:52585580..52585613,-p3@ATP7B
Hg19::chr14:70278539..70278553,+p@chr14:70278539..70278553
+
Hg19::chr16:80654831..80654863,-p@chr16:80654831..80654863
-
Hg19::chr16:87983093..87983105,+p@chr16:87983093..87983105
+
Hg19::chr19:15162579..15162588,+p5@CASP14
Hg19::chr19:34810421..34810430,+p@chr19:34810421..34810430
+
Hg19::chr19:3914342..3914345,-p@chr19:3914342..3914345
-
Hg19::chr19:54180020..54180022,+p@chr19:54180020..54180022
+
Hg19::chr19:54183760..54183765,+p@chr19:54183760..54183765
+
Hg19::chr19:55488197..55488199,+p@chr19:55488197..55488199
+
Hg19::chr1:160990524..160990546,-p@chr1:160990524..160990546
-
Hg19::chr1:92371839..92371867,-p11@TGFBR3
Hg19::chr20:62439413..62439432,+p1@ENST00000435912
Hg19::chr21:44345659..44345670,-p3@uc002zco.2
Hg19::chr2:126468524..126468553,+p3@ENST00000430692
Hg19::chr2:131058236..131058275,-p@chr2:131058236..131058275
-
Hg19::chr3:133174942..133174952,-p4@ENST00000515542
p4@uc003epo.2
Hg19::chr3:176634728..176634764,-p@chr3:176634728..176634764
-
Hg19::chr3:36853841..36853850,-p@chr3:36853841..36853850
-
Hg19::chr3:48519267..48519301,-p@chr3:48519267..48519301
-
Hg19::chr4:25452431..25452441,-p@chr4:25452431..25452441
-
Hg19::chr4:25452454..25452465,-p@chr4:25452454..25452465
-
Hg19::chr4:8582113..8582129,+p4@GPR78
Hg19::chr5:172721722..172721748,-p1@ENST00000501670
Hg19::chr6:107009148..107009180,+p@chr6:107009148..107009180
+
Hg19::chr6:157357555..157357574,+p@chr6:157357555..157357574
+
Hg19::chr6:158121413..158121421,+p@chr6:158121413..158121421
+
Hg19::chr6:53007664..53007669,-p@chr6:53007664..53007669
-
Hg19::chr7:92107256..92107265,-p@chr7:92107256..92107265
-
Hg19::chr7:99321090..99321095,+p@chr7:99321090..99321095
+
Hg19::chr8:143844567..143844588,+p2@ENST00000523657
Hg19::chr8:42360015..42360030,-p20@SLC20A2
Hg19::chr9:133968754..133968762,-p@chr9:133968754..133968762
-
Hg19::chr9:78949005..78949024,-p@chr9:78949005..78949024
-
Hg19::chrX:119709377..119709392,-p16@CUL4B
Hg19::chrX:135618258..135618269,+p6@VGLL1
Hg19::chrX:152990686..152990697,+p6@ABCD1


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:0015919peroxisomal membrane transport0.0309961144471918
GO:0015677copper ion import0.0309961144471918
GO:0022804active transmembrane transporter activity0.0425695048000345
GO:0005315inorganic phosphate transmembrane transporter activity0.0425695048000345
GO:0043682copper-transporting ATPase activity0.0425695048000345
GO:0004008copper-exporting ATPase activity0.0425695048000345
GO:0046688response to copper ion0.0425695048000345
GO:0005436sodium:phosphate symporter activity0.0425695048000345
GO:0006878cellular copper ion homeostasis0.0425695048000345
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0425695048000345
GO:0043492ATPase activity, coupled to movement of substances0.0425695048000345
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0425695048000345
GO:0051208sequestering of calcium ion0.0425695048000345
GO:0015399primary active transmembrane transporter activity0.0425695048000345
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0425695048000345
GO:0055070copper ion homeostasis0.0425695048000345
GO:0051238sequestering of metal ion0.0450057037700196
GO:0015114phosphate transmembrane transporter activity0.0450057037700196
GO:0005375copper ion transmembrane transporter activity0.0450057037700196
GO:0005779integral to peroxisomal membrane0.0450057037700196
GO:0031231intrinsic to peroxisomal membrane0.0450057037700196
GO:0043574peroxisomal transport0.0450057037700196
GO:0031461cullin-RING ubiquitin ligase complex0.0494829688645146
GO:0006825copper ion transport0.0494829688645146
GO:0031625ubiquitin protein ligase binding0.0494829688645146
GO:0005802trans-Golgi network0.0499528863193797



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
germ line cell1.70e-507
germ cell1.70e-507
chorionic membrane mesenchymal stem cell1.21e-083
epithelial cell of pancreas6.50e-074
Uber Anatomy
Ontology termp-valuen
chorion1.49e-137
acellular anatomical structure1.21e-083
egg chorion1.21e-083
extraembryonic membrane3.04e-0714
membranous layer3.04e-0714
placenta8.14e-074
allantois8.14e-074


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)
MA0003.10.0154222
MA0004.10.30839
MA0006.10.0335907
MA0007.10.278299
MA0009.10.263756
MA0014.10.000271547
MA0017.10.745976
MA0019.12.02765
MA0024.10.565136
MA0025.10.3631
MA0027.11.74826
MA0028.10.040096
MA0029.10.206098
MA0030.10.577011
MA0031.10.935558
MA0038.10.495033
MA0040.10.603427
MA0041.12.36639
MA0042.12.14038
MA0043.10.263979
MA0046.10.256123
MA0048.10.0627077
MA0050.10.120463
MA0051.10.0624698
MA0052.10.21238
MA0055.10.065659
MA0056.10
MA0057.10.356136
MA0058.10.564942
MA0059.10.333736
MA0060.10.515898
MA0061.10.562179
MA0063.10
MA0066.10.229222
MA0067.10.514146
MA0068.10.151529
MA0069.10.253439
MA0070.10.245703
MA0071.10.188714
MA0072.10.24262
MA0073.14.43878e-07
MA0074.11.26806
MA0076.10.015898
MA0077.10.237364
MA0078.10.694373
MA0081.10.0634322
MA0083.10.269067
MA0084.10.679402
MA0087.10.240948
MA0088.10.119947
MA0089.10
MA0090.10.663659
MA0091.10.90132
MA0092.10.765858
MA0093.10.216325
MA0095.10
MA0098.10
MA0100.10.0692891
MA0101.10.887871
MA0103.10.810916
MA0105.10.699163
MA0106.10.275063
MA0107.10.545054
MA0108.21.48467
MA0109.10
MA0111.11.04431
MA0113.10.61348
MA0114.10.523499
MA0115.10.449785
MA0116.11.37776
MA0117.10.290704
MA0119.10.14837
MA0122.10.309767
MA0124.10.415762
MA0125.10.349207
MA0130.10
MA0131.11.20643
MA0132.10
MA0133.10
MA0135.10.285448
MA0136.10.236422
MA0139.10.00230374
MA0140.10.415677
MA0141.11.17489
MA0142.10.436942
MA0143.10.294674
MA0144.10.0351305
MA0145.10.158153
MA0146.10.018018
MA0147.10.118849
MA0148.10.630483
MA0149.10.0465992
MA0062.20.011479
MA0035.20.72943
MA0039.20.0396411
MA0138.21.15143
MA0002.20.102327
MA0137.20.0429195
MA0104.20.0562978
MA0047.20.553745
MA0112.20.819888
MA0065.20.246505
MA0150.10.0787122
MA0151.10
MA0152.10.1926
MA0153.10.336269
MA0154.13.02343
MA0155.10.176093
MA0156.10.123394
MA0157.10.796344
MA0158.10
MA0159.12.1494
MA0160.11.04202
MA0161.10
MA0162.12.70925e-05
MA0163.10.120423
MA0164.10.309505
MA0080.20.216477
MA0018.20.276679
MA0099.20.0519295
MA0079.25.38778e-09
MA0102.20.713248
MA0258.12.12315
MA0259.10.406874
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
GATA3#262595.002625453364376.53641175906428e-050.00106101384473875



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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