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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C269_Basophils_Mast_Eosinophils_mature_CD14_chorionic_CD4
|full_id=C269_Basophils_Mast_Eosinophils_mature_CD14_chorionic_CD4
|gostat_on_coexpression_clusters=GO:0046983!protein dimerization activity!0.00711510319422719!2354;2353$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.00711510319422719!2354;2353$GO:0006366!transcription from RNA polymerase II promoter!0.0108672074601084!2354;2353$GO:0043565!sequence-specific DNA binding!0.0151367636305051!2354;2353$GO:0006306!DNA methylation!0.0207554734031237!2353$GO:0006305!DNA alkylation!0.0207554734031237!2353$GO:0006304!DNA modification!0.0210525571751405!2353$GO:0003700!transcription factor activity!0.0210525571751405!2354;2353$GO:0004289!subtilase activity!0.0210525571751405!2354$GO:0003704!specific RNA polymerase II transcription factor activity!0.0211114637320105!2353$GO:0043414!biopolymer methylation!0.0221429353030901!2353$GO:0040029!regulation of gene expression, epigenetic!0.0293102504025579!2353$GO:0032259!methylation!0.0299662068333565!2353$GO:0007275!multicellular organismal development!0.0300828750979383!2354;2353$GO:0046982!protein heterodimerization activity!0.0365019430155593!2353$GO:0003690!double-stranded DNA binding!0.0365019430155593!2353$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0377712194593578!2354$GO:0006730!one-carbon compound metabolic process!0.0377712194593578!2353$GO:0043566!structure-specific DNA binding!0.0377712194593578!2353$GO:0032502!developmental process!0.0377712194593578!2354;2353$GO:0006355!regulation of transcription, DNA-dependent!0.0377712194593578!2354;2353$GO:0006351!transcription, DNA-dependent!0.0377712194593578!2354;2353$GO:0032774!RNA biosynthetic process!0.0377712194593578!2354;2353$GO:0003677!DNA binding!0.0377712194593578!2354;2353$GO:0045449!regulation of transcription!0.0377712194593578!2354;2353$GO:0045892!negative regulation of transcription, DNA-dependent!0.0377712194593578!2354$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0377712194593578!2354;2353$GO:0005667!transcription factor complex!0.0377712194593578!2353$GO:0006350!transcription!0.0377712194593578!2354;2353$GO:0032501!multicellular organismal process!0.0377712194593578!2354;2353$GO:0010468!regulation of gene expression!0.0377712194593578!2354;2353$GO:0031323!regulation of cellular metabolic process!0.0385252847918647!2354;2353$GO:0019222!regulation of metabolic process!0.0404684885098427!2354;2353$GO:0016070!RNA metabolic process!0.0404684885098427!2354;2353$GO:0003702!RNA polymerase II transcription factor activity!0.0417237654697631!2353$GO:0006954!inflammatory response!0.0417237654697631!2353$GO:0016481!negative regulation of transcription!0.0417237654697631!2354$GO:0007610!behavior!0.0417237654697631!2354$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0440945903855701!2354$GO:0004252!serine-type endopeptidase activity!0.0448697405908615!2354$GO:0008236!serine-type peptidase activity!0.0477218639162913!2354$GO:0017171!serine hydrolase activity!0.0477218639162913!2354$GO:0031324!negative regulation of cellular metabolic process!0.0477218639162913!2354
|id=C269
|id=C269
}}
}}

Revision as of 17:37, 18 May 2012


Full id: C269_Basophils_Mast_Eosinophils_mature_CD14_chorionic_CD4



Phase1 CAGE Peaks

Hg19::chr14:75745523..75745537,+p1@FOS
Hg19::chr14:75745802..75745826,-p@chr14:75745802..75745826
-
Hg19::chr14:75746579..75746605,+p9@FOS
Hg19::chr14:75746613..75746623,+p11@FOS
Hg19::chr14:75746687..75746702,+p10@FOS
Hg19::chr14:75746705..75746720,+p8@FOS
Hg19::chr14:75746722..75746777,+p2@FOS
Hg19::chr14:75746781..75746799,+p6@FOS
Hg19::chr14:75747250..75747267,+p5@FOS
Hg19::chr14:75747296..75747329,+p4@FOS
Hg19::chr14:75747492..75747516,+p@chr14:75747492..75747516
+
Hg19::chr14:75747550..75747561,+p@chr14:75747550..75747561
+
Hg19::chr14:75747573..75747583,+p@chr14:75747573..75747583
+
Hg19::chr14:75747611..75747620,+p@chr14:75747611..75747620
+
Hg19::chr14:75747625..75747645,+p@chr14:75747625..75747645
+
Hg19::chr14:75747656..75747717,+p@chr14:75747656..75747717
+
Hg19::chr14:75747782..75747798,+p@chr14:75747782..75747798
+
Hg19::chr14:75747827..75747836,+p@chr14:75747827..75747836
+
Hg19::chr14:75747960..75747972,+p@chr14:75747960..75747972
+
Hg19::chr14:75748018..75748039,+p@chr14:75748018..75748039
+
Hg19::chr14:75748187..75748202,+p@chr14:75748187..75748202
+
Hg19::chr14:75748263..75748319,+p@chr14:75748263..75748319
+
Hg19::chr14:75748371..75748442,+p1@S65140
Hg19::chr14:75748616..75748661,+p2@S65140
Hg19::chr19:45972203..45972226,+p5@FOSB
Hg19::chr19:45973899..45973920,+p@chr19:45973899..45973920
+
Hg19::chr19:45973962..45973979,+p@chr19:45973962..45973979
+
Hg19::chr19:45974005..45974026,+p11@FOSB
Hg19::chr19:45974032..45974054,+p9@FOSB
Hg19::chr19:45974146..45974170,+p7@FOSB
Hg19::chr19:45974438..45974449,+p26@FOSB
Hg19::chr19:45975749..45975760,+p@chr19:45975749..45975760
+
Hg19::chr19:45975995..45976038,+p2@AF432216
Hg19::chr19:45976177..45976190,+p6@AF432216
Hg19::chr19:45976666..45976678,+p3@AF432216
Hg19::chr19:45977115..45977124,+p@chr19:45977115..45977124
+
Hg19::chr19:45977207..45977222,+p@chr19:45977207..45977222
+
Hg19::chr19:45977304..45977312,+p@chr19:45977304..45977312
+
Hg19::chr19:45977321..45977334,+p@chr19:45977321..45977334
+
Hg19::chr19:45977344..45977355,+p@chr19:45977344..45977355
+
Hg19::chr19:45977475..45977486,+p@chr19:45977475..45977486
+
Hg19::chr19:45977515..45977522,+p@chr19:45977515..45977522
+
Hg19::chr19:45977611..45977627,+p@chr19:45977611..45977627
+
Hg19::chr19:45977632..45977642,+p@chr19:45977632..45977642
+
Hg19::chr19:45977697..45977713,+p4@FOSB
Hg19::chr19:45977759..45977770,+p10@FOSB
Hg19::chr19:45977916..45977932,+p13@FOSB
Hg19::chr19:45977993..45978005,+p6@FOSB
Hg19::chr19:45978061..45978070,+p24@FOSB


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:0046983protein dimerization activity0.00711510319422719
GO:0006357regulation of transcription from RNA polymerase II promoter0.00711510319422719
GO:0006366transcription from RNA polymerase II promoter0.0108672074601084
GO:0043565sequence-specific DNA binding0.0151367636305051
GO:0006306DNA methylation0.0207554734031237
GO:0006305DNA alkylation0.0207554734031237
GO:0006304DNA modification0.0210525571751405
GO:0003700transcription factor activity0.0210525571751405
GO:0004289subtilase activity0.0210525571751405
GO:0003704specific RNA polymerase II transcription factor activity0.0211114637320105
GO:0043414biopolymer methylation0.0221429353030901
GO:0040029regulation of gene expression, epigenetic0.0293102504025579
GO:0032259methylation0.0299662068333565
GO:0007275multicellular organismal development0.0300828750979383
GO:0046982protein heterodimerization activity0.0365019430155593
GO:0003690double-stranded DNA binding0.0365019430155593
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0377712194593578
GO:0006730one-carbon compound metabolic process0.0377712194593578
GO:0043566structure-specific DNA binding0.0377712194593578
GO:0032502developmental process0.0377712194593578
GO:0006355regulation of transcription, DNA-dependent0.0377712194593578
GO:0006351transcription, DNA-dependent0.0377712194593578
GO:0032774RNA biosynthetic process0.0377712194593578
GO:0003677DNA binding0.0377712194593578
GO:0045449regulation of transcription0.0377712194593578
GO:0045892negative regulation of transcription, DNA-dependent0.0377712194593578
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0377712194593578
GO:0005667transcription factor complex0.0377712194593578
GO:0006350transcription0.0377712194593578
GO:0032501multicellular organismal process0.0377712194593578
GO:0010468regulation of gene expression0.0377712194593578
GO:0031323regulation of cellular metabolic process0.0385252847918647
GO:0019222regulation of metabolic process0.0404684885098427
GO:0016070RNA metabolic process0.0404684885098427
GO:0003702RNA polymerase II transcription factor activity0.0417237654697631
GO:0006954inflammatory response0.0417237654697631
GO:0016481negative regulation of transcription0.0417237654697631
GO:0007610behavior0.0417237654697631
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0440945903855701
GO:0004252serine-type endopeptidase activity0.0448697405908615
GO:0008236serine-type peptidase activity0.0477218639162913
GO:0017171serine hydrolase activity0.0477218639162913
GO:0031324negative regulation of cellular metabolic process0.0477218639162913



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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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