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MCL coexpression mm9:3384: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0043038;amino acid activation;5.53017928454632e-05;107271,20226!GO:0043039;tRNA aminoacylation;5.53017928454632e-05;107271,20226!GO:0006418;tRNA aminoacylation for protein translation;5.53017928454632e-05;107271,20226!GO:0016876;ligase activity, forming aminoacyl-tRNA and related compounds;5.53017928454632e-05;107271,20226!GO:0016875;ligase activity, forming carbon-oxygen bonds;5.53017928454632e-05;107271,20226!GO:0004812;aminoacyl-tRNA ligase activity;5.53017928454632e-05;107271,20226!GO:0006399;tRNA metabolic process;0.000199521774478894;107271,20226!GO:0006520;amino acid metabolic process;0.000803815791288871;107271,20226!GO:0006434;seryl-tRNA aminoacylation;0.000858282884454908;20226!GO:0004828;serine-tRNA ligase activity;0.000858282884454908;20226!GO:0004831;tyrosine-tRNA ligase activity;0.000858282884454908;107271!GO:0006437;tyrosyl-tRNA aminoacylation;0.000858282884454908;107271!GO:0006519;amino acid and derivative metabolic process;0.00085993419714682;107271,20226!GO:0016874;ligase activity;0.00100874984582194;107271,20226!GO:0009308;amine metabolic process;0.00100874984582194;107271,20226!GO:0006807;nitrogen compound metabolic process;0.00109559623274966;107271,20226!GO:0006412;translation;0.00148691136252163;107271,20226!GO:0019752;carboxylic acid metabolic process;0.00148691136252163;107271,20226!GO:0006082;organic acid metabolic process;0.00148691136252163;107271,20226!GO:0009059;macromolecule biosynthetic process;0.00288472209210212;107271,20226!GO:0000049;tRNA binding;0.00294187802669021;107271!GO:0044249;cellular biosynthetic process;0.0045300786801657;107271,20226!GO:0009058;biosynthetic process;0.00793648198463862;107271,20226!GO:0005524;ATP binding;0.00876794125052577;107271,20226!GO:0032559;adenyl ribonucleotide binding;0.00876794125052577;107271,20226!GO:0030554;adenyl nucleotide binding;0.00929024541403085;107271,20226!GO:0032553;ribonucleotide binding;0.0121595522398973;107271,20226!GO:0032555;purine ribonucleotide binding;0.0121595522398973;107271,20226!GO:0017076;purine nucleotide binding;0.0126960618437547;107271,20226!GO:0000166;nucleotide binding;0.0157397084846313;107271,20226!GO:0016070;RNA metabolic process;0.0223576884150985;107271,20226!GO:0044267;cellular protein metabolic process;0.029193421430314;107271,20226!GO:0044260;cellular macromolecule metabolic process;0.029193421430314;107271,20226!GO:0010467;gene expression;0.029193421430314;107271,20226!GO:0019538;protein metabolic process;0.02967869063179;107271,20226!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0335849292761187;107271,20226!
|gostat_on_MCL_coexpression=GO:0043038;amino acid activation;5.53017928454632e-05;107271,20226!GO:0043039;tRNA aminoacylation;5.53017928454632e-05;107271,20226!GO:0006418;tRNA aminoacylation for protein translation;5.53017928454632e-05;107271,20226!GO:0016876;ligase activity, forming aminoacyl-tRNA and related compounds;5.53017928454632e-05;107271,20226!GO:0016875;ligase activity, forming carbon-oxygen bonds;5.53017928454632e-05;107271,20226!GO:0004812;aminoacyl-tRNA ligase activity;5.53017928454632e-05;107271,20226!GO:0006399;tRNA metabolic process;0.000199521774478894;107271,20226!GO:0006520;amino acid metabolic process;0.000803815791288871;107271,20226!GO:0006434;seryl-tRNA aminoacylation;0.000858282884454908;20226!GO:0004828;serine-tRNA ligase activity;0.000858282884454908;20226!GO:0004831;tyrosine-tRNA ligase activity;0.000858282884454908;107271!GO:0006437;tyrosyl-tRNA aminoacylation;0.000858282884454908;107271!GO:0006519;amino acid and derivative metabolic process;0.00085993419714682;107271,20226!GO:0016874;ligase activity;0.00100874984582194;107271,20226!GO:0009308;amine metabolic process;0.00100874984582194;107271,20226!GO:0006807;nitrogen compound metabolic process;0.00109559623274966;107271,20226!GO:0006412;translation;0.00148691136252163;107271,20226!GO:0019752;carboxylic acid metabolic process;0.00148691136252163;107271,20226!GO:0006082;organic acid metabolic process;0.00148691136252163;107271,20226!GO:0009059;macromolecule biosynthetic process;0.00288472209210212;107271,20226!GO:0000049;tRNA binding;0.00294187802669021;107271!GO:0044249;cellular biosynthetic process;0.0045300786801657;107271,20226!GO:0009058;biosynthetic process;0.00793648198463862;107271,20226!GO:0005524;ATP binding;0.00876794125052577;107271,20226!GO:0032559;adenyl ribonucleotide binding;0.00876794125052577;107271,20226!GO:0030554;adenyl nucleotide binding;0.00929024541403085;107271,20226!GO:0032553;ribonucleotide binding;0.0121595522398973;107271,20226!GO:0032555;purine ribonucleotide binding;0.0121595522398973;107271,20226!GO:0017076;purine nucleotide binding;0.0126960618437547;107271,20226!GO:0000166;nucleotide binding;0.0157397084846313;107271,20226!GO:0016070;RNA metabolic process;0.0223576884150985;107271,20226!GO:0044267;cellular protein metabolic process;0.029193421430314;107271,20226!GO:0044260;cellular macromolecule metabolic process;0.029193421430314;107271,20226!GO:0010467;gene expression;0.029193421430314;107271,20226!GO:0019538;protein metabolic process;0.02967869063179;107271,20226!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0335849292761187;107271,20226!
}}
}}

Revision as of 13:28, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr3:108248065..108248096,-p1@Sars
Mm9::chr3:108248101..108248129,-p2@Sars
Mm9::chr4:128867107..128867200,+p1@Yars


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:0043038amino acid activation5.53017928454632e-05
GO:0043039tRNA aminoacylation5.53017928454632e-05
GO:0006418tRNA aminoacylation for protein translation5.53017928454632e-05
GO:0016876ligase activity, forming aminoacyl-tRNA and related compounds5.53017928454632e-05
GO:0016875ligase activity, forming carbon-oxygen bonds5.53017928454632e-05
GO:0004812aminoacyl-tRNA ligase activity5.53017928454632e-05
GO:0006399tRNA metabolic process0.000199521774478894
GO:0006520amino acid metabolic process0.000803815791288871
GO:0006434seryl-tRNA aminoacylation0.000858282884454908
GO:0004828serine-tRNA ligase activity0.000858282884454908
GO:0004831tyrosine-tRNA ligase activity0.000858282884454908
GO:0006437tyrosyl-tRNA aminoacylation0.000858282884454908
GO:0006519amino acid and derivative metabolic process0.00085993419714682
GO:0016874ligase activity0.00100874984582194
GO:0009308amine metabolic process0.00100874984582194
GO:0006807nitrogen compound metabolic process0.00109559623274966
GO:0006412translation0.00148691136252163
GO:0019752carboxylic acid metabolic process0.00148691136252163
GO:0006082organic acid metabolic process0.00148691136252163
GO:0009059macromolecule biosynthetic process0.00288472209210212
GO:0000049tRNA binding0.00294187802669021
GO:0044249cellular biosynthetic process0.0045300786801657
GO:0009058biosynthetic process0.00793648198463862
GO:0005524ATP binding0.00876794125052577
GO:0032559adenyl ribonucleotide binding0.00876794125052577
GO:0030554adenyl nucleotide binding0.00929024541403085
GO:0032553ribonucleotide binding0.0121595522398973
GO:0032555purine ribonucleotide binding0.0121595522398973
GO:0017076purine nucleotide binding0.0126960618437547
GO:0000166nucleotide binding0.0157397084846313
GO:0016070RNA metabolic process0.0223576884150985
GO:0044267cellular protein metabolic process0.029193421430314
GO:0044260cellular macromolecule metabolic process0.029193421430314
GO:0010467gene expression0.029193421430314
GO:0019538protein metabolic process0.02967869063179
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0335849292761187



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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