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

Latest revision as of 11:21, 17 September 2013


Full id: C360_Placental_Amniotic_amniotic_teratocarcinoma_chorionic_neuroblastoma_H9



Phase1 CAGE Peaks

Hg19::chr11:1971324..1971344,+p@chr11:1971324..1971344
+
Hg19::chr11:1982869..1982890,+p@chr11:1982869..1982890
+
Hg19::chr11:62370454..62370468,-p@chr11:62370454..62370468
-
Hg19::chr11:62370475..62370497,-p@chr11:62370475..62370497
-
Hg19::chr11:62370516..62370535,-p@chr11:62370516..62370535
-
Hg19::chr14:104202647..104202662,-p@chr14:104202647..104202662
-
Hg19::chr14:24729174..24729183,-p17@TGM1
Hg19::chr17:37824217..37824226,+p12@PNMT
Hg19::chr17:37824259..37824278,+p1@PNMT
Hg19::chr19:1513576..1513590,-p2@ADAMTSL5
Hg19::chr19:36592925..36592948,+p@chr19:36592925..36592948
+
Hg19::chr19:36592959..36592975,+p@chr19:36592959..36592975
+
Hg19::chr19:36592982..36592993,+p@chr19:36592982..36592993
+
Hg19::chr1:161044552..161044633,-p2@PVRL4
Hg19::chr1:27339317..27339375,-p1@FAM46B
Hg19::chr20:61288222..61288232,+p14@SLCO4A1
Hg19::chr20:61288249..61288259,+p12@SLCO4A1
Hg19::chr4:177592751..177592777,-p@chr4:177592751..177592777
-
Hg19::chr5:153854787..153854796,-p@chr5:153854787..153854796
-
Hg19::chr5:153854814..153854825,-p@chr5:153854814..153854825
-
Hg19::chr5:153855055..153855066,-p@chr5:153855055..153855066
-
Hg19::chr5:153855212..153855222,-p@chr5:153855212..153855222
-
Hg19::chr5:153857778..153857794,-p1@HAND1
Hg19::chr5:153857800..153857812,-p2@HAND1
Hg19::chr5:153857819..153857824,-p3@HAND1
Hg19::chr5:153858046..153858049,+p@chr5:153858046..153858049
+
Hg19::chr5:153858071..153858085,+p@chr5:153858071..153858085
+
Hg19::chr7:29603436..29603471,+p1@PRR15
Hg19::chr7:29603477..29603510,+p2@PRR15
Hg19::chr7:29603521..29603533,+p4@PRR15
Hg19::chr7:29603552..29603566,+p5@PRR15


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:0048729tissue morphogenesis0.00775487924830703
GO:0006576biogenic amine metabolic process0.00775487924830703
GO:0006575amino acid derivative metabolic process0.00775487924830703
GO:0004603phenylethanolamine N-methyltransferase activity0.0082935947250677
GO:0043163cell envelope organization and biogenesis0.0110571497501241
GO:0015349thyroid hormone transmembrane transporter activity0.0110571497501241
GO:0009888tissue development0.0351980101711255
GO:0042423catecholamine biosynthetic process0.0351980101711255
GO:0009887organ morphogenesis0.0351980101711255
GO:0042403thyroid hormone metabolic process0.0351980101711255
GO:0005913cell-cell adherens junction0.0351980101711255
GO:0003810protein-glutamine gamma-glutamyltransferase activity0.0351980101711255
GO:0001707mesoderm formation0.0351980101711255
GO:0030054cell junction0.0351980101711255
GO:0048332mesoderm morphogenesis0.0351980101711255
GO:0001704formation of primary germ layer0.0351980101711255
GO:0045229external encapsulating structure organization and biogenesis0.0388545276905836
GO:0001533cornified envelope0.0388545276905836
GO:0007369gastrulation0.0388545276905836
GO:0006519amino acid and derivative metabolic process0.0388545276905836
GO:0018149peptide cross-linking0.0388545276905836
GO:0006584catecholamine metabolic process0.0388545276905836
GO:0018958phenol metabolic process0.0388545276905836
GO:0030216keratinocyte differentiation0.0413619195937827
GO:0009308amine metabolic process0.0432556527482064
GO:0042401biogenic amine biosynthetic process0.0432556527482064
GO:0031424keratinization0.0449337123578184
GO:0006807nitrogen compound metabolic process0.0449337123578184
GO:0016755transferase activity, transferring amino-acyl groups0.0454419119423075
GO:0042398amino acid derivative biosynthetic process0.0454419119423075
GO:0007275multicellular organismal development0.0454419119423075
GO:0007498mesoderm development0.0454419119423075
GO:0009913epidermal cell differentiation0.048575240672889
GO:0008170N-methyltransferase activity0.048575240672889



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>

Disease
Ontology termp-valuen
vascular disease1.06e-091
ischemia1.06e-091
extrinsic cardiomyopathy1.06e-091
myocardial ischemia1.06e-091
myocardial infarction1.06e-091


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)
MA0003.10.695878
MA0004.11.05161
MA0006.10.124841
MA0007.14.79101
MA0009.10.406485
MA0014.11.76956
MA0017.10.662194
MA0019.10.514288
MA0024.10.322368
MA0025.10.520106
MA0027.11.94566
MA0028.10.0349277
MA0029.10.337465
MA0030.10.328486
MA0031.10.279263
MA0038.10.446179
MA0040.10.342075
MA0041.10.0995936
MA0042.10.0842644
MA0043.10.406746
MA0046.10.397506
MA0048.11.56421
MA0050.10.0846723
MA0051.10.439954
MA0052.10.345132
MA0055.13.50585
MA0056.10
MA0057.12.56292
MA0058.10.421253
MA0059.10.418621
MA0060.11.28384
MA0061.10.18834
MA0063.10
MA0066.11.41106
MA0067.10.685278
MA0068.10.821915
MA0069.10.394339
MA0070.10.385179
MA0071.10.123343
MA0072.10.381514
MA0073.16.65524
MA0074.10.142444
MA0076.10.0564857
MA0077.10.37525
MA0078.10.592477
MA0081.10.0502365
MA0083.10.412707
MA0084.10.860109
MA0087.10.379524
MA0088.10.492869
MA0089.10
MA0090.10.223118
MA0091.10.0917987
MA0092.12.52883
MA0093.10.878362
MA0095.10
MA0098.10
MA0100.10.153602
MA0101.10.130624
MA0103.10.519443
MA0105.10.604146
MA0106.10.170405
MA0107.10.185157
MA0108.20.759502
MA0109.10
MA0111.10.880329
MA0113.11.61805
MA0114.12.06483
MA0115.10.615724
MA0116.10.371987
MA0117.10.437859
MA0119.10.686178
MA0122.11.16324
MA0124.10.578498
MA0125.10.50452
MA0130.10
MA0131.10.217579
MA0132.10
MA0133.10
MA0135.10.431776
MA0136.10.456636
MA0139.10.0738384
MA0140.10.773759
MA0141.10.415079
MA0142.10.255934
MA0143.11.02251
MA0144.10.157126
MA0145.12.15486
MA0146.10.154565
MA0147.10.630118
MA0148.10.102785
MA0149.10.116654
MA0062.20.080735
MA0035.20.385357
MA0039.25.07588
MA0138.20.20609
MA0002.20.219603
MA0137.20.145957
MA0104.20.242912
MA0047.20.162866
MA0112.20.527714
MA0065.21.87212
MA0150.10.0597704
MA0151.10
MA0152.10.125496
MA0153.10.489927
MA0154.13.07991
MA0155.11.61978
MA0156.10.148172
MA0157.10.236372
MA0158.10
MA0159.10.632503
MA0160.10.110614
MA0161.10
MA0162.10.0869856
MA0163.13.28482
MA0164.10.188828
MA0080.20.127678
MA0018.20.510438
MA0099.20.790611
MA0079.23.86107
MA0102.20.895427
MA0258.10.763055
MA0259.11.35555
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
CTBP2#148836.06938712961240.01305028938831740.0463008857365383



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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