Personal tools

Difference between revisions of "Coexpression cluster:C360"

From FANTOM5_SSTAR

Jump to: navigation, search
Line 3: Line 3:
 
|gostat_on_coexpression_clusters=GO:0048729!tissue morphogenesis!0.00775487924830703!7051;9421$GO:0006576!biogenic amine metabolic process!0.00775487924830703!28231;5409$GO:0006575!amino acid derivative metabolic process!0.00775487924830703!28231;5409$GO:0004603!phenylethanolamine N-methyltransferase activity!0.0082935947250677!5409$GO:0043163!cell envelope organization and biogenesis!0.0110571497501241!7051$GO:0015349!thyroid hormone transmembrane transporter activity!0.0110571497501241!28231$GO:0009888!tissue development!0.0351980101711255!7051;9421$GO:0042423!catecholamine biosynthetic process!0.0351980101711255!5409$GO:0009887!organ morphogenesis!0.0351980101711255!7051;9421$GO:0042403!thyroid hormone metabolic process!0.0351980101711255!28231$GO:0005913!cell-cell adherens junction!0.0351980101711255!7051$GO:0003810!protein-glutamine gamma-glutamyltransferase activity!0.0351980101711255!7051$GO:0001707!mesoderm formation!0.0351980101711255!9421$GO:0030054!cell junction!0.0351980101711255!81607;7051$GO:0048332!mesoderm morphogenesis!0.0351980101711255!9421$GO:0001704!formation of primary germ layer!0.0351980101711255!9421$GO:0045229!external encapsulating structure organization and biogenesis!0.0388545276905836!7051$GO:0001533!cornified envelope!0.0388545276905836!7051$GO:0007369!gastrulation!0.0388545276905836!9421$GO:0006519!amino acid and derivative metabolic process!0.0388545276905836!28231;5409$GO:0018149!peptide cross-linking!0.0388545276905836!7051$GO:0006584!catecholamine metabolic process!0.0388545276905836!5409$GO:0018958!phenol metabolic process!0.0388545276905836!5409$GO:0030216!keratinocyte differentiation!0.0413619195937827!7051$GO:0009308!amine metabolic process!0.0432556527482064!28231;5409$GO:0042401!biogenic amine biosynthetic process!0.0432556527482064!5409$GO:0031424!keratinization!0.0449337123578184!7051$GO:0006807!nitrogen compound metabolic process!0.0449337123578184!28231;5409$GO:0016755!transferase activity, transferring amino-acyl groups!0.0454419119423075!7051$GO:0042398!amino acid derivative biosynthetic process!0.0454419119423075!5409$GO:0007275!multicellular organismal development!0.0454419119423075!222171;7051;9421$GO:0007498!mesoderm development!0.0454419119423075!9421$GO:0009913!epidermal cell differentiation!0.048575240672889!7051$GO:0008170!N-methyltransferase activity!0.048575240672889!5409
 
|gostat_on_coexpression_clusters=GO:0048729!tissue morphogenesis!0.00775487924830703!7051;9421$GO:0006576!biogenic amine metabolic process!0.00775487924830703!28231;5409$GO:0006575!amino acid derivative metabolic process!0.00775487924830703!28231;5409$GO:0004603!phenylethanolamine N-methyltransferase activity!0.0082935947250677!5409$GO:0043163!cell envelope organization and biogenesis!0.0110571497501241!7051$GO:0015349!thyroid hormone transmembrane transporter activity!0.0110571497501241!28231$GO:0009888!tissue development!0.0351980101711255!7051;9421$GO:0042423!catecholamine biosynthetic process!0.0351980101711255!5409$GO:0009887!organ morphogenesis!0.0351980101711255!7051;9421$GO:0042403!thyroid hormone metabolic process!0.0351980101711255!28231$GO:0005913!cell-cell adherens junction!0.0351980101711255!7051$GO:0003810!protein-glutamine gamma-glutamyltransferase activity!0.0351980101711255!7051$GO:0001707!mesoderm formation!0.0351980101711255!9421$GO:0030054!cell junction!0.0351980101711255!81607;7051$GO:0048332!mesoderm morphogenesis!0.0351980101711255!9421$GO:0001704!formation of primary germ layer!0.0351980101711255!9421$GO:0045229!external encapsulating structure organization and biogenesis!0.0388545276905836!7051$GO:0001533!cornified envelope!0.0388545276905836!7051$GO:0007369!gastrulation!0.0388545276905836!9421$GO:0006519!amino acid and derivative metabolic process!0.0388545276905836!28231;5409$GO:0018149!peptide cross-linking!0.0388545276905836!7051$GO:0006584!catecholamine metabolic process!0.0388545276905836!5409$GO:0018958!phenol metabolic process!0.0388545276905836!5409$GO:0030216!keratinocyte differentiation!0.0413619195937827!7051$GO:0009308!amine metabolic process!0.0432556527482064!28231;5409$GO:0042401!biogenic amine biosynthetic process!0.0432556527482064!5409$GO:0031424!keratinization!0.0449337123578184!7051$GO:0006807!nitrogen compound metabolic process!0.0449337123578184!28231;5409$GO:0016755!transferase activity, transferring amino-acyl groups!0.0454419119423075!7051$GO:0042398!amino acid derivative biosynthetic process!0.0454419119423075!5409$GO:0007275!multicellular organismal development!0.0454419119423075!222171;7051;9421$GO:0007498!mesoderm development!0.0454419119423075!9421$GO:0009913!epidermal cell differentiation!0.048575240672889!7051$GO:0008170!N-methyltransferase activity!0.048575240672889!5409
 
|id=C360
 
|id=C360
 +
|ontology_enrichment_celltype=CL:0000066!4.23e-16!254;CL:0002076!9.03e-09!43;CL:0000223!3.05e-07!59
 +
|ontology_enrichment_disease=DOID:305!1.05e-11!106;DOID:0050687!2.82e-08!143
 +
|ontology_enrichment_uberon=UBERON:0004119!2.63e-15!169;UBERON:0000925!2.63e-15!169;UBERON:0006595!2.63e-15!169;UBERON:0000468!3.35e-13!659;UBERON:0004921!1.21e-12!129;UBERON:0004185!1.21e-12!129;UBERON:0001007!5.57e-12!155;UBERON:0001555!5.57e-12!155;UBERON:0007026!5.57e-12!155;UBERON:0000077!1.70e-11!130;UBERON:0000062!1.84e-11!511;UBERON:0000466!2.10e-11!126;UBERON:0000464!2.15e-11!104;UBERON:0003104!8.17e-11!238;UBERON:0009142!8.17e-11!238;UBERON:0000481!3.38e-09!347;UBERON:0009569!9.24e-09!113;UBERON:0005631!1.07e-08!14;UBERON:0000158!1.07e-08!14;UBERON:0004923!3.06e-08!57;UBERON:0000480!5.19e-08!626;UBERON:0000467!6.91e-08!625;UBERON:0000922!8.56e-08!612;UBERON:0003103!1.03e-07!69;UBERON:0002100!1.31e-07!216;UBERON:0000064!1.82e-07!219;UBERON:0000478!1.90e-07!24;UBERON:0001048!2.09e-07!168;UBERON:0001041!2.19e-07!98;UBERON:0002553!2.38e-07!70;UBERON:0005177!4.23e-07!107;UBERON:0001004!5.27e-07!72
 
}}
 
}}

Revision as of 05:38, 21 May 2012


Full id: C360_Placental_Amniotic_amniotic_teratocarcinoma_chorionic_neuroblastoma_H9



Phase1 CAGE Peaks

  Short description
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 clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
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 clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
epithelial cell4.23e-16254
endo-epithelial cell9.03e-0943
endodermal cell3.05e-0759
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.63e-15169
endoderm2.63e-15169
presumptive endoderm2.63e-15169
multi-cellular organism3.35e-13659
subdivision of digestive tract1.21e-12129
endodermal part of digestive tract1.21e-12129
digestive system5.57e-12155
digestive tract5.57e-12155
primitive gut5.57e-12155
mixed endoderm/mesoderm-derived structure1.70e-11130
organ1.84e-11511
immaterial anatomical entity2.10e-11126
anatomical space2.15e-11104
mesenchyme8.17e-11238
entire embryonic mesenchyme8.17e-11238
multi-tissue structure3.38e-09347
subdivision of trunk9.24e-09113
extraembryonic membrane1.07e-0814
membranous layer1.07e-0814
organ component layer3.06e-0857
anatomical group5.19e-08626
anatomical system6.91e-08625
embryo8.56e-08612
compound organ1.03e-0769
trunk1.31e-07216
organ part1.82e-07219
extraembryonic structure1.90e-0724
primordium2.09e-07168
foregut2.19e-0798
anatomical cavity2.38e-0770
trunk region element4.23e-07107
respiratory system5.27e-0772
Disease
Ontology termp-valuen
carcinoma1.05e-11106
cell type cancer2.82e-08143


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.