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MCL coexpression mm9:946: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0006551;leucine metabolic process;0.00905712736433923;!GO:0003884;D-amino-acid oxidase activity;0.00905712736433923;!GO:0046087;cytidine metabolic process;0.00905712736433923;72269!GO:0046131;pyrimidine ribonucleoside metabolic process;0.0101884308949003;72269!GO:0004126;cytidine deaminase activity;0.010866766470503;72269!GO:0006213;pyrimidine nucleoside metabolic process;0.0118825956045149;72269!GO:0009119;ribonucleoside metabolic process;0.0118825956045149;72269!GO:0009081;branched chain family amino acid metabolic process;0.0118825956045149;!GO:0016641;oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor;0.0237378594464625;!GO:0009116;nucleoside metabolic process;0.0237378594464625;72269!GO:0016638;oxidoreductase activity, acting on the CH-NH2 group of donors;0.0237378594464625;!GO:0019239;deaminase activity;0.0237378594464625;72269!GO:0016814;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines;0.0239947699080005;72269!
|gostat_on_MCL_coexpression=GO:0006551;leucine metabolic process;0.00905712736433923;!GO:0003884;D-amino-acid oxidase activity;0.00905712736433923;!GO:0046087;cytidine metabolic process;0.00905712736433923;72269!GO:0046131;pyrimidine ribonucleoside metabolic process;0.0101884308949003;72269!GO:0004126;cytidine deaminase activity;0.010866766470503;72269!GO:0006213;pyrimidine nucleoside metabolic process;0.0118825956045149;72269!GO:0009119;ribonucleoside metabolic process;0.0118825956045149;72269!GO:0009081;branched chain family amino acid metabolic process;0.0118825956045149;!GO:0016641;oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor;0.0237378594464625;!GO:0009116;nucleoside metabolic process;0.0237378594464625;72269!GO:0016638;oxidoreductase activity, acting on the CH-NH2 group of donors;0.0237378594464625;!GO:0019239;deaminase activity;0.0237378594464625;72269!GO:0016814;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines;0.0239947699080005;72269!
}}
}}

Revision as of 12:49, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr13:35055660..35055685,-p1@Eci3
Mm9::chr13:35055694..35055705,-p2@Eci3
Mm9::chr2:166885638..166885674,-p@chr2:166885638..166885674
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Mm9::chr4:137923796..137923807,-p@chr4:137923796..137923807
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Mm9::chr4:94316783..94316818,-p1@Lrrc19
Mm9::chr4:94316825..94316840,-p2@Lrrc19
Mm9::chr5:114454790..114454818,+p3@Dao
Mm9::chr9:107507434..107507453,-p@chr9:107507434..107507453
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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:0006551leucine metabolic process0.00905712736433923
GO:0003884D-amino-acid oxidase activity0.00905712736433923
GO:0046087cytidine metabolic process0.00905712736433923
GO:0046131pyrimidine ribonucleoside metabolic process0.0101884308949003
GO:0004126cytidine deaminase activity0.010866766470503
GO:0006213pyrimidine nucleoside metabolic process0.0118825956045149
GO:0009119ribonucleoside metabolic process0.0118825956045149
GO:0009081branched chain family amino acid metabolic process0.0118825956045149
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.0237378594464625
GO:0009116nucleoside metabolic process0.0237378594464625
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.0237378594464625
GO:0019239deaminase activity0.0237378594464625
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0239947699080005



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>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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)

{{{tfbs_overrepresentation_jaspar}}}

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