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Coexpression cluster:C494: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C494_occipital_medial_brain_Whole_caudate_parietal_blood
|full_id=C494_occipital_medial_brain_Whole_caudate_parietal_blood
|gostat_on_coexpression_clusters=GO:0005517!calmodulin inhibitor activity!0.00382662447319203!5534$GO:0004723!calcium-dependent protein serine/threonine phosphatase activity!0.00382662447319203!5534$GO:0005955!calcineurin complex!0.0051020157702358!5534$GO:0005313!L-glutamate transmembrane transporter activity!0.00650382537410799!6506$GO:0015172!acidic amino acid transmembrane transporter activity!0.00650382537410799!6506$GO:0015813!L-glutamate transport!0.00650382537410799!6506$GO:0015800!acidic amino acid transport!0.00650382537410799!6506$GO:0017153!sodium:dicarboxylate symporter activity!0.00650382537410799!6506$GO:0005310!dicarboxylic acid transmembrane transporter activity!0.00650382537410799!6506$GO:0006835!dicarboxylic acid transport!0.00650382537410799!6506$GO:0015179!L-amino acid transmembrane transporter activity!0.0111270830268056!6506$GO:0005343!organic acid:sodium symporter activity!0.011473621593484!6506$GO:0015296!anion:cation symporter activity!0.011473621593484!6506$GO:0008287!protein serine/threonine phosphatase complex!0.0155312468165728!5534$GO:0015171!amino acid transmembrane transporter activity!0.0155312468165728!6506$GO:0004722!protein serine/threonine phosphatase activity!0.0155312468165728!5534$GO:0006865!amino acid transport!0.0157409186351371!6506$GO:0015837!amine transport!0.0164476067567351!6506$GO:0015370!solute:sodium symporter activity!0.0164476067567351!6506$GO:0046943!carboxylic acid transmembrane transporter activity!0.0164476067567351!6506$GO:0046942!carboxylic acid transport!0.0164476067567351!6506$GO:0015849!organic acid transport!0.0164476067567351!6506$GO:0005342!organic acid transmembrane transporter activity!0.0164476067567351!6506$GO:0015294!solute:cation symporter activity!0.018146502540626!6506$GO:0005516!calmodulin binding!0.0215380072397654!5534$GO:0008509!anion transmembrane transporter activity!0.0306664547475256!6506$GO:0015293!symporter activity!0.0341767369167349!6506$GO:0007268!synaptic transmission!0.0394648935897162!6506$GO:0004721!phosphoprotein phosphatase activity!0.0411120977212879!5534$GO:0019226!transmission of nerve impulse!0.0418896566957398!6506$GO:0015291!secondary active transmembrane transporter activity!0.0442040623661732!6506
|id=C494
|id=C494
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C494_occipital_medial_brain_Whole_caudate_parietal_blood



Phase1 CAGE Peaks

Hg19::chr11:124615395..124615405,+p@chr11:124615395..124615405
+
Hg19::chr11:124615417..124615426,+p@chr11:124615417..124615426
+
Hg19::chr11:124615444..124615454,+p@chr11:124615444..124615454
+
Hg19::chr11:124615466..124615503,+p@chr11:124615466..124615503
+
Hg19::chr11:124615584..124615600,+p@chr11:124615584..124615600
+
Hg19::chr11:124616294..124616374,+p@chr11:124616294..124616374
+
Hg19::chr11:124616375..124616422,+p@chr11:124616375..124616422
+
Hg19::chr11:124616427..124616476,+p@chr11:124616427..124616476
+
Hg19::chr11:124616482..124616540,+p@chr11:124616482..124616540
+
Hg19::chr11:124616552..124616569,+p@chr11:124616552..124616569
+
Hg19::chr11:124616611..124616623,+p@chr11:124616611..124616623
+
Hg19::chr11:124616640..124616647,+p@chr11:124616640..124616647
+
Hg19::chr11:124616709..124616718,+p@chr11:124616709..124616718
+
Hg19::chr11:35275624..35275635,-p14@SLC1A2
Hg19::chr11:35277083..35277090,-p47@SLC1A2
Hg19::chr12:49389153..49389154,-p@chr12:49389153..49389154
-
Hg19::chr16:743961..743974,-p@chr16:743961..743974
-
Hg19::chr2:68479697..68479708,-p2@PPP3R1
Hg19::chr8:21939098..21939104,+p@chr8:21939098..21939104
+


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:0005517calmodulin inhibitor activity0.00382662447319203
GO:0004723calcium-dependent protein serine/threonine phosphatase activity0.00382662447319203
GO:0005955calcineurin complex0.0051020157702358
GO:0005313L-glutamate transmembrane transporter activity0.00650382537410799
GO:0015172acidic amino acid transmembrane transporter activity0.00650382537410799
GO:0015813L-glutamate transport0.00650382537410799
GO:0015800acidic amino acid transport0.00650382537410799
GO:0017153sodium:dicarboxylate symporter activity0.00650382537410799
GO:0005310dicarboxylic acid transmembrane transporter activity0.00650382537410799
GO:0006835dicarboxylic acid transport0.00650382537410799
GO:0015179L-amino acid transmembrane transporter activity0.0111270830268056
GO:0005343organic acid:sodium symporter activity0.011473621593484
GO:0015296anion:cation symporter activity0.011473621593484
GO:0008287protein serine/threonine phosphatase complex0.0155312468165728
GO:0015171amino acid transmembrane transporter activity0.0155312468165728
GO:0004722protein serine/threonine phosphatase activity0.0155312468165728
GO:0006865amino acid transport0.0157409186351371
GO:0015837amine transport0.0164476067567351
GO:0015370solute:sodium symporter activity0.0164476067567351
GO:0046943carboxylic acid transmembrane transporter activity0.0164476067567351
GO:0046942carboxylic acid transport0.0164476067567351
GO:0015849organic acid transport0.0164476067567351
GO:0005342organic acid transmembrane transporter activity0.0164476067567351
GO:0015294solute:cation symporter activity0.018146502540626
GO:0005516calmodulin binding0.0215380072397654
GO:0008509anion transmembrane transporter activity0.0306664547475256
GO:0015293symporter activity0.0341767369167349
GO:0007268synaptic transmission0.0394648935897162
GO:0004721phosphoprotein phosphatase activity0.0411120977212879
GO:0019226transmission of nerve impulse0.0418896566957398
GO:0015291secondary active transmembrane transporter activity0.0442040623661732



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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