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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C2359_cord_cerebellum_occipital_frontal_parietal_postcentral_brain
|full_id=C2359_cord_cerebellum_occipital_frontal_parietal_postcentral_brain
|gostat_on_coexpression_clusters=GO:0016595!glutamate binding!0.0144622987337513!2903$GO:0008328!ionotropic glutamate receptor complex!0.0144622987337513!2903$GO:0017146!N-methyl-D-aspartate selective glutamate receptor complex!0.0144622987337513!2903$GO:0004972!N-methyl-D-aspartate selective glutamate receptor activity!0.0144622987337513!2903$GO:0004115!3',5'-cyclic-AMP phosphodiesterase activity!0.0144622987337513!5142$GO:0007613!memory!0.0177063306952289!2903$GO:0042734!presynaptic membrane!0.0177063306952289!2903$GO:0048167!regulation of synaptic plasticity!0.0180704237443215!2903$GO:0050803!regulation of synapse structure and activity!0.0180704237443215!2903$GO:0016597!amino acid binding!0.0180704237443215!2903$GO:0005626!insoluble fraction!0.0180704237443215!5142$GO:0007215!glutamate signaling pathway!0.0180704237443215!2903$GO:0006695!cholesterol biosynthetic process!0.0198552699367001!51422$GO:0016126!sterol biosynthetic process!0.0225114542956761!51422$GO:0004970!ionotropic glutamate receptor activity!0.0225114542956761!2903$GO:0005234!extracellular-glutamate-gated ion channel activity!0.0225114542956761!2903$GO:0007611!learning and/or memory!0.0225114542956761!2903$GO:0043176!amine binding!0.0225114542956761!2903$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase activity!0.0225114542956761!5142$GO:0004112!cyclic-nucleotide phosphodiesterase activity!0.0225114542956761!5142$GO:0005977!glycogen metabolic process!0.0225114542956761!51422$GO:0006073!glucan metabolic process!0.0225114542956761!51422$GO:0006112!energy reserve metabolic process!0.0246677940691695!51422$GO:0005231!excitatory extracellular ligand-gated ion channel activity!0.0284869167389958!2903$GO:0006633!fatty acid biosynthetic process!0.0284869167389958!51422$GO:0008203!cholesterol metabolic process!0.0284869167389958!51422$GO:0043005!neuron projection!0.0284869167389958!2903$GO:0016053!organic acid biosynthetic process!0.0284869167389958!51422$GO:0046394!carboxylic acid biosynthetic process!0.0284869167389958!51422$GO:0044264!cellular polysaccharide metabolic process!0.0284869167389958!51422$GO:0005976!polysaccharide metabolic process!0.0284869167389958!51422$GO:0006694!steroid biosynthetic process!0.0284869167389958!51422$GO:0016125!sterol metabolic process!0.0284869167389958!51422$GO:0008066!glutamate receptor activity!0.0284869167389958!2903$GO:0043235!receptor complex!0.0323680396493635!2903$GO:0015980!energy derivation by oxidation of organic compounds!0.033464591504368!51422$GO:0005230!extracellular ligand-gated ion channel activity!0.0364411892024579!2903$GO:0008081!phosphoric diester hydrolase activity!0.0373704950705004!5142$GO:0045211!postsynaptic membrane!0.039301958964788!2903$GO:0044456!synapse part!0.0401508769760526!2903$GO:0015276!ligand-gated ion channel activity!0.0401508769760526!2903$GO:0022834!ligand-gated channel activity!0.0401508769760526!2903$GO:0006631!fatty acid metabolic process!0.0456372653621256!51422
|id=C2359
|id=C2359
}}
}}

Revision as of 17:37, 18 May 2012


Full id: C2359_cord_cerebellum_occipital_frontal_parietal_postcentral_brain



Phase1 CAGE Peaks

Hg19::chr16:10276731..10276772,-p1@GRIN2A
Hg19::chr16:10277298..10277308,-p@chr16:10277298..10277308
-
Hg19::chr1:66820232..66820259,+p22@PDE4B
Hg19::chr7:151511577..151511596,-p25@PRKAG2


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:0016595glutamate binding0.0144622987337513
GO:0008328ionotropic glutamate receptor complex0.0144622987337513
GO:0017146N-methyl-D-aspartate selective glutamate receptor complex0.0144622987337513
GO:0004972N-methyl-D-aspartate selective glutamate receptor activity0.0144622987337513
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.0144622987337513
GO:0007613memory0.0177063306952289
GO:0042734presynaptic membrane0.0177063306952289
GO:0048167regulation of synaptic plasticity0.0180704237443215
GO:0050803regulation of synapse structure and activity0.0180704237443215
GO:0016597amino acid binding0.0180704237443215
GO:0005626insoluble fraction0.0180704237443215
GO:0007215glutamate signaling pathway0.0180704237443215
GO:0006695cholesterol biosynthetic process0.0198552699367001
GO:0016126sterol biosynthetic process0.0225114542956761
GO:0004970ionotropic glutamate receptor activity0.0225114542956761
GO:0005234extracellular-glutamate-gated ion channel activity0.0225114542956761
GO:0007611learning and/or memory0.0225114542956761
GO:0043176amine binding0.0225114542956761
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0225114542956761
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0225114542956761
GO:0005977glycogen metabolic process0.0225114542956761
GO:0006073glucan metabolic process0.0225114542956761
GO:0006112energy reserve metabolic process0.0246677940691695
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0284869167389958
GO:0006633fatty acid biosynthetic process0.0284869167389958
GO:0008203cholesterol metabolic process0.0284869167389958
GO:0043005neuron projection0.0284869167389958
GO:0016053organic acid biosynthetic process0.0284869167389958
GO:0046394carboxylic acid biosynthetic process0.0284869167389958
GO:0044264cellular polysaccharide metabolic process0.0284869167389958
GO:0005976polysaccharide metabolic process0.0284869167389958
GO:0006694steroid biosynthetic process0.0284869167389958
GO:0016125sterol metabolic process0.0284869167389958
GO:0008066glutamate receptor activity0.0284869167389958
GO:0043235receptor complex0.0323680396493635
GO:0015980energy derivation by oxidation of organic compounds0.033464591504368
GO:0005230extracellular ligand-gated ion channel activity0.0364411892024579
GO:0008081phosphoric diester hydrolase activity0.0373704950705004
GO:0045211postsynaptic membrane0.039301958964788
GO:0044456synapse part0.0401508769760526
GO:0015276ligand-gated ion channel activity0.0401508769760526
GO:0022834ligand-gated channel activity0.0401508769760526
GO:0006631fatty acid metabolic process0.0456372653621256



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.