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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C323_Placental_Amniotic_neuroblastoma_amniotic_chorionic_hairy_locus
|full_id=C323_Placental_Amniotic_neuroblastoma_amniotic_chorionic_hairy_locus
|gostat_on_coexpression_clusters=GO:0004511!tyrosine 3-monooxygenase activity!0.0237309072152451!7054$GO:0017166!vinculin binding!0.0237309072152451!5829$GO:0006461!protein complex assembly!0.0237309072152451!5829;2702$GO:0007154!cell communication!0.0237309072152451!9905;5829;2702;7054$GO:0035050!embryonic heart tube development!0.0237309072152451!2702$GO:0042423!catecholamine biosynthetic process!0.0240901397280719!7054$GO:0016714!oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen!0.0240901397280719!7054$GO:0007043!intercellular junction assembly!0.0240901397280719!2702$GO:0042136!neurotransmitter biosynthetic process!0.0240901397280719!7054$GO:0007172!signal complex assembly!0.0240901397280719!5829$GO:0045216!intercellular junction assembly and maintenance!0.0240901397280719!2702$GO:0007028!cytoplasm organization and biogenesis!0.0240901397280719!2702$GO:0065003!macromolecular complex assembly!0.0240901397280719!5829;2702$GO:0006584!catecholamine metabolic process!0.0240901397280719!7054$GO:0018958!phenol metabolic process!0.0240901397280719!7054$GO:0005922!connexon complex!0.0240901397280719!2702$GO:0022607!cellular component assembly!0.0240901397280719!5829;2702$GO:0042133!neurotransmitter metabolic process!0.0240901397280719!7054$GO:0030326!embryonic limb morphogenesis!0.0240901397280719!2702$GO:0035113!embryonic appendage morphogenesis!0.0240901397280719!2702$GO:0005921!gap junction!0.0240901397280719!2702$GO:0042401!biogenic amine biosynthetic process!0.0240901397280719!7054$GO:0060173!limb development!0.0240901397280719!2702$GO:0035107!appendage morphogenesis!0.0240901397280719!2702$GO:0035108!limb morphogenesis!0.0240901397280719!2702$GO:0048736!appendage development!0.0240901397280719!2702$GO:0042398!amino acid derivative biosynthetic process!0.0263269511231556!7054$GO:0009653!anatomical structure morphogenesis!0.0265091461685086!2702;7054$GO:0014704!intercalated disc!0.0265091461685086!2702$GO:0009072!aromatic amino acid family metabolic process!0.0265091461685086!7054$GO:0043623!cellular protein complex assembly!0.0376256946416683!5829$GO:0006576!biogenic amine metabolic process!0.0390825555738343!7054$GO:0001505!regulation of neurotransmitter levels!0.0399397314359315!7054$GO:0006575!amino acid derivative metabolic process!0.0439818193873885!7054$GO:0048598!embryonic morphogenesis!0.0439818193873885!2702$GO:0007507!heart development!0.0439818193873885!2702$GO:0003008!system process!0.0439818193873885!2702;7054$GO:0007160!cell-matrix adhesion!0.0439818193873885!5829$GO:0031589!cell-substrate adhesion!0.0445776803648569!5829$GO:0035295!tube development!0.0472129969561992!2702$GO:0009309!amine biosynthetic process!0.0472129969561992!7054$GO:0032313!regulation of Rab GTPase activity!0.0472129969561992!9905$GO:0032483!regulation of Rab protein signal transduction!0.0472129969561992!9905$GO:0032482!Rab protein signal transduction!0.0472129969561992!9905$GO:0005097!Rab GTPase activator activity!0.0472129969561992!9905
|id=C323
|id=C323
}}
}}

Revision as of 17:38, 18 May 2012


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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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)

{{{tfbs_overrepresentation_jaspar}}}



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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