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

Latest revision as of 11:20, 17 September 2013


Full id: C323_Placental_Amniotic_neuroblastoma_amniotic_chorionic_hairy_locus



Phase1 CAGE Peaks

Hg19::chr11:16893031..16893035,-p@chr11:16893031..16893035
-
Hg19::chr11:16893073..16893090,-p@chr11:16893073..16893090
-
Hg19::chr11:16947179..16947259,-p@chr11:16947179..16947259
-
Hg19::chr11:2011185..2011202,-p1@MRPL23-AS1
Hg19::chr11:2188016..2188030,-p2@TH
Hg19::chr11:2193037..2193053,-p1@TH
Hg19::chr12:120686548..120686582,-p14@PXN
Hg19::chr14:104202639..104202646,-p@chr14:104202639..104202646
-
Hg19::chr14:104202674..104202690,-p@chr14:104202674..104202690
-
Hg19::chr14:69095369..69095386,-p3@ENST00000556301
Hg19::chr16:3038260..3038264,+p@chr16:3038260..3038264
+
Hg19::chr16:81679150..81679182,+p17@CMIP
Hg19::chr16:81679223..81679271,+p@chr16:81679223..81679271
+
Hg19::chr17:2278539..2278556,+p6@SGSM2
Hg19::chr19:36592910..36592917,+p@chr19:36592910..36592917
+
Hg19::chr1:114522973..114522995,+p@chr1:114522973..114522995
+
Hg19::chr1:114523008..114523020,+p@chr1:114523008..114523020
+
Hg19::chr1:147232729..147232730,-p9@GJA5
Hg19::chr1:209704573..209704587,+p@chr1:209704573..209704587
+
Hg19::chr1:209704612..209704625,+p@chr1:209704612..209704625
+
Hg19::chr1:209704633..209704641,+p@chr1:209704633..209704641
+
Hg19::chr1:209704648..209704656,+p@chr1:209704648..209704656
+
Hg19::chr2:237682954..237682971,+p@chr2:237682954..237682971
+
Hg19::chr2:237682972..237682977,+p@chr2:237682972..237682977
+
Hg19::chr2:237682990..237683009,+p@chr2:237682990..237683009
+
Hg19::chr2:237683020..237683029,+p@chr2:237683020..237683029
+
Hg19::chr2:237683038..237683048,+p@chr2:237683038..237683048
+
Hg19::chr2:237683109..237683120,+p@chr2:237683109..237683120
+
Hg19::chr2:237683156..237683171,+p@chr2:237683156..237683171
+
Hg19::chr2:237683203..237683210,+p@chr2:237683203..237683210
+
Hg19::chr2:237683212..237683239,+p@chr2:237683212..237683239
+
Hg19::chr3:55518443..55518474,-p@chr3:55518443..55518474
-
Hg19::chr5:89143573..89143607,-p@chr5:89143573..89143607
-
Hg19::chr7:29603266..29603282,-p1@ENST00000447171
p1@uc003tab.2
Hg19::chr8:27995319..27995365,+p@chr8:27995319..27995365
+
Hg19::chr9:88126069..88126080,-p@chr9:88126069..88126080
-


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:0004511tyrosine 3-monooxygenase activity0.0237309072152451
GO:0017166vinculin binding0.0237309072152451
GO:0006461protein complex assembly0.0237309072152451
GO:0007154cell communication0.0237309072152451
GO:0035050embryonic heart tube development0.0237309072152451
GO:0042423catecholamine biosynthetic process0.0240901397280719
GO:0016714oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen0.0240901397280719
GO:0007043intercellular junction assembly0.0240901397280719
GO:0042136neurotransmitter biosynthetic process0.0240901397280719
GO:0007172signal complex assembly0.0240901397280719
GO:0045216intercellular junction assembly and maintenance0.0240901397280719
GO:0007028cytoplasm organization and biogenesis0.0240901397280719
GO:0065003macromolecular complex assembly0.0240901397280719
GO:0006584catecholamine metabolic process0.0240901397280719
GO:0018958phenol metabolic process0.0240901397280719
GO:0005922connexon complex0.0240901397280719
GO:0022607cellular component assembly0.0240901397280719
GO:0042133neurotransmitter metabolic process0.0240901397280719
GO:0030326embryonic limb morphogenesis0.0240901397280719
GO:0035113embryonic appendage morphogenesis0.0240901397280719
GO:0005921gap junction0.0240901397280719
GO:0042401biogenic amine biosynthetic process0.0240901397280719
GO:0060173limb development0.0240901397280719
GO:0035107appendage morphogenesis0.0240901397280719
GO:0035108limb morphogenesis0.0240901397280719
GO:0048736appendage development0.0240901397280719
GO:0042398amino acid derivative biosynthetic process0.0263269511231556
GO:0009653anatomical structure morphogenesis0.0265091461685086
GO:0014704intercalated disc0.0265091461685086
GO:0009072aromatic amino acid family metabolic process0.0265091461685086
GO:0043623cellular protein complex assembly0.0376256946416683
GO:0006576biogenic amine metabolic process0.0390825555738343
GO:0001505regulation of neurotransmitter levels0.0399397314359315
GO:0006575amino acid derivative metabolic process0.0439818193873885
GO:0048598embryonic morphogenesis0.0439818193873885
GO:0007507heart development0.0439818193873885
GO:0003008system process0.0439818193873885
GO:0007160cell-matrix adhesion0.0439818193873885
GO:0031589cell-substrate adhesion0.0445776803648569
GO:0035295tube development0.0472129969561992
GO:0009309amine biosynthetic process0.0472129969561992
GO:0032313regulation of Rab GTPase activity0.0472129969561992
GO:0032483regulation of Rab protein signal transduction0.0472129969561992
GO:0032482Rab protein signal transduction0.0472129969561992
GO:0005097Rab GTPase activator activity0.0472129969561992



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>


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)
MA0003.10.0613148
MA0004.10.0673987
MA0006.10.0866247
MA0007.11.24502
MA0009.10.357426
MA0014.10.0020986
MA0017.10.117334
MA0019.10.139271
MA0024.10.27745
MA0025.10.466941
MA0027.11.88112
MA0028.10.0227941
MA0029.10.793017
MA0030.11.41281
MA0031.10.236975
MA0038.10.367847
MA0040.10.29608
MA0041.10.260286
MA0042.10.0621361
MA0043.10.357676
MA0046.10.348837
MA0048.15.0681
MA0050.10.224248
MA0051.10.112588
MA0052.10.298977
MA0055.12.64563
MA0056.10
MA0057.11.10595
MA0058.10.139468
MA0059.10.323594
MA0060.11.31642
MA0061.10.0514741
MA0063.10
MA0066.10.114994
MA0067.10.628098
MA0068.10.40606
MA0069.10.34581
MA0070.10.337064
MA0071.10.0954724
MA0072.10.333568
MA0073.18.01489e-06
MA0074.10.112201
MA0076.10.0394639
MA0077.10.327598
MA0078.10.168619
MA0081.10.0345295
MA0083.10.363385
MA0084.10.800231
MA0087.10.331671
MA0088.10.0728668
MA0089.10
MA0090.11.05254
MA0091.10.068452
MA0092.11.17586
MA0093.10.0888338
MA0095.10
MA0098.10
MA0100.10.386851
MA0101.10.228124
MA0103.10.204359
MA0105.10.0475651
MA0106.10.840244
MA0107.10.261512
MA0108.20.23485
MA0109.10
MA0111.12.07751
MA0113.10.880211
MA0114.10.25082
MA0115.10.560015
MA0116.12.19257
MA0117.10.387522
MA0119.12.71679
MA0122.10.408619
MA0124.10.523698
MA0125.10.451839
MA0130.10
MA0131.10.179874
MA0132.10
MA0133.10
MA0135.10.381677
MA0136.10.118463
MA0139.10.00194292
MA0140.10.64656
MA0141.10.0340013
MA0142.10.215252
MA0143.10.146532
MA0144.10.221855
MA0145.10.25161
MA0146.10.33755
MA0147.10.1348
MA0148.10.267923
MA0149.10.0896745
MA0062.20.047645
MA0035.20.644966
MA0039.20.00611105
MA0138.20.169371
MA0002.21.94092
MA0137.20.253969
MA0104.20.0730367
MA0047.20.408085
MA0112.20.14127
MA0065.20.053355
MA0150.11.02856
MA0151.10
MA0152.10.0973462
MA0153.10.43772
MA0154.10.161618
MA0155.10.421257
MA0156.10.0247505
MA0157.10.197151
MA0158.10
MA0159.10.732547
MA0160.10.286561
MA0161.10
MA0162.10.0341129
MA0163.10.479991
MA0164.10.153683
MA0080.20.088897
MA0018.20.427256
MA0099.20.322107
MA0079.22.53969e-06
MA0102.20.835136
MA0258.10.203344
MA0259.10.145321
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
NR3C1#290872.911421203283650.008862197712668590.033626124138543



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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