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MCL coexpression mm9:912: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0019919;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;0.00848079767709418;15469!GO:0016275;[cytochrome c]-arginine N-methyltransferase activity;0.00848079767709418;15469!GO:0035242;protein-arginine omega-N asymmetric methyltransferase activity;0.00848079767709418;15469!GO:0035247;peptidyl-arginine omega-N-methylation;0.00848079767709418;15469!GO:0035241;protein-arginine omega-N monomethyltransferase activity;0.00848079767709418;15469!GO:0018216;peptidyl-arginine methylation;0.0115615562661957;15469!GO:0035246;peptidyl-arginine N-methylation;0.0115615562661957;15469!GO:0016273;arginine N-methyltransferase activity;0.0115615562661957;15469!GO:0018195;peptidyl-arginine modification;0.0115615562661957;15469!GO:0008469;histone-arginine N-methyltransferase activity;0.0115615562661957;15469!GO:0016274;protein-arginine N-methyltransferase activity;0.0115615562661957;15469!GO:0043193;positive regulation of gene-specific transcription;0.0117724336002034;21849!GO:0003677;DNA binding;0.0117724336002034;21849,228839,67781,20833!GO:0045449;regulation of transcription;0.0117724336002034;21849,228839,67781,20833!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0117724336002034;21849,228839,67781,20833!GO:0006350;transcription;0.0117724336002034;21849,228839,67781,20833!GO:0000785;chromatin;0.0117724336002034;21849,20833!GO:0032583;regulation of gene-specific transcription;0.0117724336002034;21849!GO:0010468;regulation of gene expression;0.0122181804073108;21849,228839,67781,20833!GO:0031323;regulation of cellular metabolic process;0.0135249862227857;21849,228839,67781,20833!GO:0019222;regulation of metabolic process;0.0147854056711222;21849,228839,67781,20833!GO:0001837;epithelial to mesenchymal transition;0.0154048542908589;21849!GO:0044427;chromosomal part;0.0216833268507031;21849,20833!GO:0010467;gene expression;0.0277227841110429;21849,228839,67781,20833!GO:0005694;chromosome;0.0277227841110429;21849,20833!GO:0003676;nucleic acid binding;0.0283307318082205;21849,228839,67781,20833!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0345708430066191;21849,228839,67781,20833!GO:0043565;sequence-specific DNA binding;0.0345708430066191;21849,228839!GO:0042054;histone methyltransferase activity;0.0345708430066191;15469!GO:0043232;intracellular non-membrane-bound organelle;0.0345708430066191;21849,67781,20833!GO:0043228;non-membrane-bound organelle;0.0345708430066191;21849,67781,20833!GO:0006479;protein amino acid methylation;0.0345708430066191;15469!GO:0008213;protein amino acid alkylation;0.0345708430066191;15469!GO:0050794;regulation of cellular process;0.0370591123014948;21849,228839,67781,20833!GO:0008170;N-methyltransferase activity;0.0387003362702759;15469!GO:0008276;protein methyltransferase activity;0.0387003362702759;15469!GO:0048762;mesenchymal cell differentiation;0.0432939771660033;21849!GO:0014031;mesenchymal cell development;0.0432939771660033;21849!GO:0043414;biopolymer methylation;0.0454101306158489;15469!GO:0050789;regulation of biological process;0.0462552943785845;21849,228839,67781,20833!GO:0032259;methylation;0.0462552943785845;15469!GO:0006355;regulation of transcription, DNA-dependent;0.0462552943785845;21849,67781,20833!GO:0006351;transcription, DNA-dependent;0.0462552943785845;21849,67781,20833!GO:0032774;RNA biosynthetic process;0.0462552943785845;21849,67781,20833!
|gostat_on_MCL_coexpression=GO:0019919;peptidyl-arginine methylation, to asymmetrical-dimethyl arginine;0.00848079767709418;15469!GO:0016275;[cytochrome c]-arginine N-methyltransferase activity;0.00848079767709418;15469!GO:0035242;protein-arginine omega-N asymmetric methyltransferase activity;0.00848079767709418;15469!GO:0035247;peptidyl-arginine omega-N-methylation;0.00848079767709418;15469!GO:0035241;protein-arginine omega-N monomethyltransferase activity;0.00848079767709418;15469!GO:0018216;peptidyl-arginine methylation;0.0115615562661957;15469!GO:0035246;peptidyl-arginine N-methylation;0.0115615562661957;15469!GO:0016273;arginine N-methyltransferase activity;0.0115615562661957;15469!GO:0018195;peptidyl-arginine modification;0.0115615562661957;15469!GO:0008469;histone-arginine N-methyltransferase activity;0.0115615562661957;15469!GO:0016274;protein-arginine N-methyltransferase activity;0.0115615562661957;15469!GO:0043193;positive regulation of gene-specific transcription;0.0117724336002034;21849!GO:0003677;DNA binding;0.0117724336002034;21849,228839,67781,20833!GO:0045449;regulation of transcription;0.0117724336002034;21849,228839,67781,20833!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0117724336002034;21849,228839,67781,20833!GO:0006350;transcription;0.0117724336002034;21849,228839,67781,20833!GO:0000785;chromatin;0.0117724336002034;21849,20833!GO:0032583;regulation of gene-specific transcription;0.0117724336002034;21849!GO:0010468;regulation of gene expression;0.0122181804073108;21849,228839,67781,20833!GO:0031323;regulation of cellular metabolic process;0.0135249862227857;21849,228839,67781,20833!GO:0019222;regulation of metabolic process;0.0147854056711222;21849,228839,67781,20833!GO:0001837;epithelial to mesenchymal transition;0.0154048542908589;21849!GO:0044427;chromosomal part;0.0216833268507031;21849,20833!GO:0010467;gene expression;0.0277227841110429;21849,228839,67781,20833!GO:0005694;chromosome;0.0277227841110429;21849,20833!GO:0003676;nucleic acid binding;0.0283307318082205;21849,228839,67781,20833!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0345708430066191;21849,228839,67781,20833!GO:0043565;sequence-specific DNA binding;0.0345708430066191;21849,228839!GO:0042054;histone methyltransferase activity;0.0345708430066191;15469!GO:0043232;intracellular non-membrane-bound organelle;0.0345708430066191;21849,67781,20833!GO:0043228;non-membrane-bound organelle;0.0345708430066191;21849,67781,20833!GO:0006479;protein amino acid methylation;0.0345708430066191;15469!GO:0008213;protein amino acid alkylation;0.0345708430066191;15469!GO:0050794;regulation of cellular process;0.0370591123014948;21849,228839,67781,20833!GO:0008170;N-methyltransferase activity;0.0387003362702759;15469!GO:0008276;protein methyltransferase activity;0.0387003362702759;15469!GO:0048762;mesenchymal cell differentiation;0.0432939771660033;21849!GO:0014031;mesenchymal cell development;0.0432939771660033;21849!GO:0043414;biopolymer methylation;0.0454101306158489;15469!GO:0050789;regulation of biological process;0.0462552943785845;21849,228839,67781,20833!GO:0032259;methylation;0.0462552943785845;15469!GO:0006355;regulation of transcription, DNA-dependent;0.0462552943785845;21849,67781,20833!GO:0006351;transcription, DNA-dependent;0.0462552943785845;21849,67781,20833!GO:0032774;RNA biosynthetic process;0.0462552943785845;21849,67781,20833!
}}
}}

Revision as of 12:48, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:68829575..68829637,+p1@1500010J02Rik
Mm9::chr2:156666727..156666753,+p2@Tgif2
Mm9::chr2:84877369..84877459,+p1@Ssrp1
Mm9::chr3:90280043..90280142,+p1@Ilf2
Mm9::chr5:31797109..31797151,+p1@Gpn1
Mm9::chr7:13609469..13609537,+p3@Trim28
Mm9::chr7:52241683..52241722,-p1@Prmt1
Mm9::chr8:81032775..81032808,-p1@Rbmxl1


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:0019919peptidyl-arginine methylation, to asymmetrical-dimethyl arginine0.00848079767709418
GO:0016275[cytochrome c]-arginine N-methyltransferase activity0.00848079767709418
GO:0035242protein-arginine omega-N asymmetric methyltransferase activity0.00848079767709418
GO:0035247peptidyl-arginine omega-N-methylation0.00848079767709418
GO:0035241protein-arginine omega-N monomethyltransferase activity0.00848079767709418
GO:0018216peptidyl-arginine methylation0.0115615562661957
GO:0035246peptidyl-arginine N-methylation0.0115615562661957
GO:0016273arginine N-methyltransferase activity0.0115615562661957
GO:0018195peptidyl-arginine modification0.0115615562661957
GO:0008469histone-arginine N-methyltransferase activity0.0115615562661957
GO:0016274protein-arginine N-methyltransferase activity0.0115615562661957
GO:0043193positive regulation of gene-specific transcription0.0117724336002034
GO:0003677DNA binding0.0117724336002034
GO:0045449regulation of transcription0.0117724336002034
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0117724336002034
GO:0006350transcription0.0117724336002034
GO:0000785chromatin0.0117724336002034
GO:0032583regulation of gene-specific transcription0.0117724336002034
GO:0010468regulation of gene expression0.0122181804073108
GO:0031323regulation of cellular metabolic process0.0135249862227857
GO:0019222regulation of metabolic process0.0147854056711222
GO:0001837epithelial to mesenchymal transition0.0154048542908589
GO:0044427chromosomal part0.0216833268507031
GO:0010467gene expression0.0277227841110429
GO:0005694chromosome0.0277227841110429
GO:0003676nucleic acid binding0.0283307318082205
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0345708430066191
GO:0043565sequence-specific DNA binding0.0345708430066191
GO:0042054histone methyltransferase activity0.0345708430066191
GO:0043232intracellular non-membrane-bound organelle0.0345708430066191
GO:0043228non-membrane-bound organelle0.0345708430066191
GO:0006479protein amino acid methylation0.0345708430066191
GO:0008213protein amino acid alkylation0.0345708430066191
GO:0050794regulation of cellular process0.0370591123014948
GO:0008170N-methyltransferase activity0.0387003362702759
GO:0008276protein methyltransferase activity0.0387003362702759
GO:0048762mesenchymal cell differentiation0.0432939771660033
GO:0014031mesenchymal cell development0.0432939771660033
GO:0043414biopolymer methylation0.0454101306158489
GO:0050789regulation of biological process0.0462552943785845
GO:0032259methylation0.0462552943785845
GO:0006355regulation of transcription, DNA-dependent0.0462552943785845
GO:0006351transcription, DNA-dependent0.0462552943785845
GO:0032774RNA biosynthetic process0.0462552943785845



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}}}