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Coexpression cluster:C4103: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C4103_heart_left_diaphragm_tongue_medial_skeletal_brain
|full_id=C4103_heart_left_diaphragm_tongue_medial_skeletal_brain
|gostat_on_coexpression_clusters=GO:0050164!oxoglutarate dehydrogenase (NADP+) activity!0.00856587778170257!4967$GO:0006101!citrate metabolic process!0.0102180544862346!50$GO:0015858!nucleoside transport!0.0102180544862346!2030$GO:0003994!aconitate hydratase activity!0.0102180544862346!50$GO:0004591!oxoglutarate dehydrogenase (succinyl-transferring) activity!0.0102180544862346!4967$GO:0044262!cellular carbohydrate metabolic process!0.0102180544862346!4967;50$GO:0005975!carbohydrate metabolic process!0.0176404857305316!4967;50$GO:0044248!cellular catabolic process!0.0176404857305316!4967;50$GO:0005337!nucleoside transmembrane transporter activity!0.0176404857305316!2030$GO:0016624!oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor!0.0176404857305316!4967$GO:0015932!nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity!0.0176404857305316!2030$GO:0006091!generation of precursor metabolites and energy!0.0176404857305316!4967;50$GO:0009056!catabolic process!0.0176404857305316!4967;50$GO:0005739!mitochondrion!0.0176404857305316!4967;50$GO:0006100!tricarboxylic acid cycle intermediate metabolic process!0.0182572018144486!50$GO:0046356!acetyl-CoA catabolic process!0.0189659602939553!50$GO:0006099!tricarboxylic acid cycle!0.0189659602939553!50$GO:0051539!4 iron, 4 sulfur cluster binding!0.0189659602939553!50$GO:0006084!acetyl-CoA metabolic process!0.0189659602939553!50$GO:0009109!coenzyme catabolic process!0.0189659602939553!50$GO:0051187!cofactor catabolic process!0.0189659602939553!50$GO:0016620!oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor!0.0189659602939553!4967$GO:0009060!aerobic respiration!0.0189659602939553!50$GO:0045333!cellular respiration!0.020666156364307!50$GO:0016903!oxidoreductase activity, acting on the aldehyde or oxo group of donors!0.0246182032524606!4967$GO:0051536!iron-sulfur cluster binding!0.0274611072022562!50$GO:0016836!hydro-lyase activity!0.0274611072022562!50$GO:0051540!metal cluster binding!0.0274611072022562!50$GO:0016835!carbon-oxygen lyase activity!0.0296050977840218!50$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0296050977840218!2030$GO:0015980!energy derivation by oxidation of organic compounds!0.0322190111754213!50$GO:0006096!glycolysis!0.0344012461821712!4967$GO:0006007!glucose catabolic process!0.0369496971186839!4967$GO:0019320!hexose catabolic process!0.0369496971186839!4967$GO:0046365!monosaccharide catabolic process!0.0369496971186839!4967$GO:0046164!alcohol catabolic process!0.0369496971186839!4967$GO:0031980!mitochondrial lumen!0.0398882641926015!4967$GO:0005759!mitochondrial matrix!0.0398882641926015!4967$GO:0044275!cellular carbohydrate catabolic process!0.0398882641926015!4967$GO:0016052!carbohydrate catabolic process!0.0398882641926015!4967$GO:0006006!glucose metabolic process!0.0398882641926015!4967
|id=C4103
|id=C4103
}}
}}

Revision as of 17:39, 18 May 2012


Full id: C4103_heart_left_diaphragm_tongue_medial_skeletal_brain



Phase1 CAGE Peaks

Hg19::chr22:41865109..41865152,+p1@ACO2
Hg19::chr6:44194733..44194752,+p6@SLC29A1
Hg19::chr7:44646162..44646176,+p3@OGDH


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:0050164oxoglutarate dehydrogenase (NADP+) activity0.00856587778170257
GO:0006101citrate metabolic process0.0102180544862346
GO:0015858nucleoside transport0.0102180544862346
GO:0003994aconitate hydratase activity0.0102180544862346
GO:0004591oxoglutarate dehydrogenase (succinyl-transferring) activity0.0102180544862346
GO:0044262cellular carbohydrate metabolic process0.0102180544862346
GO:0005975carbohydrate metabolic process0.0176404857305316
GO:0044248cellular catabolic process0.0176404857305316
GO:0005337nucleoside transmembrane transporter activity0.0176404857305316
GO:0016624oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor0.0176404857305316
GO:0015932nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity0.0176404857305316
GO:0006091generation of precursor metabolites and energy0.0176404857305316
GO:0009056catabolic process0.0176404857305316
GO:0005739mitochondrion0.0176404857305316
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.0182572018144486
GO:0046356acetyl-CoA catabolic process0.0189659602939553
GO:0006099tricarboxylic acid cycle0.0189659602939553
GO:00515394 iron, 4 sulfur cluster binding0.0189659602939553
GO:0006084acetyl-CoA metabolic process0.0189659602939553
GO:0009109coenzyme catabolic process0.0189659602939553
GO:0051187cofactor catabolic process0.0189659602939553
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.0189659602939553
GO:0009060aerobic respiration0.0189659602939553
GO:0045333cellular respiration0.020666156364307
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0246182032524606
GO:0051536iron-sulfur cluster binding0.0274611072022562
GO:0016836hydro-lyase activity0.0274611072022562
GO:0051540metal cluster binding0.0274611072022562
GO:0016835carbon-oxygen lyase activity0.0296050977840218
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0296050977840218
GO:0015980energy derivation by oxidation of organic compounds0.0322190111754213
GO:0006096glycolysis0.0344012461821712
GO:0006007glucose catabolic process0.0369496971186839
GO:0019320hexose catabolic process0.0369496971186839
GO:0046365monosaccharide catabolic process0.0369496971186839
GO:0046164alcohol catabolic process0.0369496971186839
GO:0031980mitochondrial lumen0.0398882641926015
GO:0005759mitochondrial matrix0.0398882641926015
GO:0044275cellular carbohydrate catabolic process0.0398882641926015
GO:0016052carbohydrate catabolic process0.0398882641926015
GO:0006006glucose metabolic process0.0398882641926015



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.