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MCL coexpression mm9:1604: Difference between revisions

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|gostat_on_MCL_coexpression=GO:0004733;pyridoxamine-phosphate oxidase activity;0.000832717011300932;103711!GO:0042819;vitamin B6 biosynthetic process;0.000832717011300932;103711!GO:0008615;pyridoxine biosynthetic process;0.000832717011300932;103711!GO:0042816;vitamin B6 metabolic process;0.000832717011300932;103711!GO:0008614;pyridoxine metabolic process;0.000832717011300932;103711!GO:0010181;FMN binding;0.00346889380409686;103711!GO:0016641;oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor;0.00416153195043072;103711!GO:0042364;water-soluble vitamin biosynthetic process;0.00416153195043072;103711!GO:0009110;vitamin biosynthetic process;0.00416153195043072;103711!GO:0016638;oxidoreductase activity, acting on the CH-NH2 group of donors;0.00416153195043072;103711!GO:0006767;water-soluble vitamin metabolic process;0.00737341938788276;103711!GO:0006766;vitamin metabolic process;0.0107382485381114;103711!GO:0050662;coenzyme binding;0.0185179814599571;103711!GO:0048037;cofactor binding;0.0248679051362699;103711!
|gostat_on_MCL_coexpression=GO:0004733;pyridoxamine-phosphate oxidase activity;0.000832717011300932;103711!GO:0042819;vitamin B6 biosynthetic process;0.000832717011300932;103711!GO:0008615;pyridoxine biosynthetic process;0.000832717011300932;103711!GO:0042816;vitamin B6 metabolic process;0.000832717011300932;103711!GO:0008614;pyridoxine metabolic process;0.000832717011300932;103711!GO:0010181;FMN binding;0.00346889380409686;103711!GO:0016641;oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor;0.00416153195043072;103711!GO:0042364;water-soluble vitamin biosynthetic process;0.00416153195043072;103711!GO:0009110;vitamin biosynthetic process;0.00416153195043072;103711!GO:0016638;oxidoreductase activity, acting on the CH-NH2 group of donors;0.00416153195043072;103711!GO:0006767;water-soluble vitamin metabolic process;0.00737341938788276;103711!GO:0006766;vitamin metabolic process;0.0107382485381114;103711!GO:0050662;coenzyme binding;0.0185179814599571;103711!GO:0048037;cofactor binding;0.0248679051362699;103711!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!6.54e-14!47;UBERON:0009854!1.62e-13!23;UBERON:0009856!1.62e-13!23;UBERON:0002107!3.87e-13!22;UBERON:0007499!3.87e-13!22;UBERON:0006925!3.87e-13!22;UBERON:0009497!3.87e-13!22;UBERON:0000015!3.87e-13!22;UBERON:0002423!3.87e-13!22;UBERON:0006235!3.87e-13!22;UBERON:0008835!3.87e-13!22;UBERON:0003894!3.87e-13!22;UBERON:0004161!3.87e-13!22;UBERON:0008836!3.87e-13!22;UBERON:0002365!1.60e-11!25;UBERON:0002330!1.60e-11!25;UBERON:0005172!6.59e-11!49;UBERON:0005173!6.59e-11!49;UBERON:0002417!6.59e-11!49;UBERON:0000916!6.59e-11!49;UBERON:0000160!4.98e-10!31;UBERON:0004119!5.50e-10!118;UBERON:0000925!5.50e-10!118;UBERON:0006595!5.50e-10!118;UBERON:0001007!8.24e-10!116;UBERON:0001555!8.24e-10!116;UBERON:0007026!8.24e-10!116;UBERON:0004921!2.20e-09!114;UBERON:0004923!2.14e-08!24
}}
}}

Revision as of 17:09, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:96805087..96805098,-p3@Pnpo
Mm9::chr11:96805100..96805111,-p4@Pnpo
Mm9::chr11:96805114..96805164,-p2@Pnpo
Mm9::chr11:96805259..96805337,-p1@Pnpo
Mm9::chr12:31596524..31596598,+p1@Sh3yl1


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

GO IDGO nameFDR corrected p-value
GO:0004733pyridoxamine-phosphate oxidase activity0.000832717011300932
GO:0042819vitamin B6 biosynthetic process0.000832717011300932
GO:0008615pyridoxine biosynthetic process0.000832717011300932
GO:0042816vitamin B6 metabolic process0.000832717011300932
GO:0008614pyridoxine metabolic process0.000832717011300932
GO:0010181FMN binding0.00346889380409686
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.00416153195043072
GO:0042364water-soluble vitamin biosynthetic process0.00416153195043072
GO:0009110vitamin biosynthetic process0.00416153195043072
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.00416153195043072
GO:0006767water-soluble vitamin metabolic process0.00737341938788276
GO:0006766vitamin metabolic process0.0107382485381114
GO:0050662coenzyme binding0.0185179814599571
GO:0048037cofactor binding0.0248679051362699



Relative expression of the co-expression cluster over median <br>Analyst:




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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
gastrointestinal system6.54e-1447
digestive tract diverticulum1.62e-1323
sac1.62e-1323
liver3.87e-1322
epithelial sac3.87e-1322
digestive gland3.87e-1322
epithelium of foregut-midgut junction3.87e-1322
anatomical boundary3.87e-1322
hepatobiliary system3.87e-1322
foregut-midgut junction3.87e-1322
hepatic diverticulum3.87e-1322
liver primordium3.87e-1322
septum transversum3.87e-1322
liver bud3.87e-1322
exocrine gland1.60e-1125
exocrine system1.60e-1125
abdomen element6.59e-1149
abdominal segment element6.59e-1149
abdominal segment of trunk6.59e-1149
abdomen6.59e-1149
intestine4.98e-1031
endoderm-derived structure5.50e-10118
endoderm5.50e-10118
presumptive endoderm5.50e-10118
digestive system8.24e-10116
digestive tract8.24e-10116
primitive gut8.24e-10116
subdivision of digestive tract2.20e-09114
organ component layer2.14e-0824


TFBS overrepresentation<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)

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