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MCL coexpression mm9:2860: Difference between revisions

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|gostat_on_MCL_coexpression=GO:0030331;estrogen receptor binding;0.00810825617706678;18193!GO:0046966;thyroid hormone receptor binding;0.00810825617706678;18193!GO:0046975;histone lysine N-methyltransferase activity (H3-K36 specific);0.00810825617706678;18193!GO:0016568;chromatin modification;0.00896215672069559;66867,18193!GO:0035258;steroid hormone receptor binding;0.00903808206770178;18193!GO:0042974;retinoic acid receptor binding;0.00903808206770178;18193!GO:0042799;histone lysine N-methyltransferase activity (H4-K20 specific);0.00903808206770178;18193!GO:0046965;retinoid X receptor binding;0.00903808206770178;18193!GO:0006325;establishment and/or maintenance of chromatin architecture;0.00903808206770178;66867,18193!GO:0017091;AU-rich element binding;0.00903808206770178;21841!GO:0006323;DNA packaging;0.00903808206770178;66867,18193!GO:0031324;negative regulation of cellular metabolic process;0.00933700986064206;21841,18193!GO:0016922;ligand-dependent nuclear receptor binding;0.00935362998129836;18193!GO:0009892;negative regulation of metabolic process;0.0102114007393278;21841,18193!GO:0051276;chromosome organization and biogenesis;0.0114543722633916;66867,18193!GO:0035097;histone methyltransferase complex;0.0114543722633916;18193!GO:0010468;regulation of gene expression;0.0114543722633916;21841,66867,18193!GO:0031323;regulation of cellular metabolic process;0.0122039355836149;21841,66867,18193!GO:0042036;negative regulation of cytokine biosynthetic process;0.0122478024990145;21841!GO:0019222;regulation of metabolic process;0.0122478024990145;21841,66867,18193!GO:0035257;nuclear hormone receptor binding;0.0127345656648945;18193!GO:0051427;hormone receptor binding;0.0132600607150388;18193!GO:0016571;histone methylation;0.0158518140714068;18193!GO:0018024;histone-lysine N-methyltransferase activity;0.0158907178865336;18193!GO:0016278;lysine N-methyltransferase activity;0.0158907178865336;18193!GO:0016279;protein-lysine N-methyltransferase activity;0.0158907178865336;18193!GO:0010467;gene expression;0.0168146204921224;21841,66867,18193!GO:0006259;DNA metabolic process;0.017233100952645;66867,18193!GO:0042054;histone methyltransferase activity;0.0198737457423813;18193!GO:0017148;negative regulation of translation;0.0198737457423813;21841!GO:0031327;negative regulation of cellular biosynthetic process;0.0198737457423813;21841!GO:0006479;protein amino acid methylation;0.0198737457423813;18193!GO:0008213;protein amino acid alkylation;0.0198737457423813;18193!GO:0001702;gastrulation with mouth forming second;0.0210871265304523;18193!GO:0050794;regulation of cellular process;0.0210871265304523;21841,66867,18193!GO:0009890;negative regulation of biosynthetic process;0.0210871265304523;21841!GO:0008170;N-methyltransferase activity;0.0210871265304523;18193!GO:0008276;protein methyltransferase activity;0.0210871265304523;18193!GO:0016570;histone modification;0.0211678896003258;18193!GO:0048523;negative regulation of cellular process;0.0216028946271842;21841,18193!GO:0016569;covalent chromatin modification;0.0219083509771772;18193!GO:0048519;negative regulation of biological process;0.0236369750219196;21841,18193!GO:0043414;biopolymer methylation;0.0236369750219196;18193!GO:0050789;regulation of biological process;0.0236369750219196;21841,66867,18193!GO:0032259;methylation;0.0242661749924914;18193!GO:0042035;regulation of cytokine biosynthetic process;0.026369046303537;21841!GO:0003714;transcription corepressor activity;0.0288954535041561;18193!GO:0065007;biological regulation;0.0289057852480629;21841,66867,18193!GO:0042089;cytokine biosynthetic process;0.0289057852480629;21841!GO:0042107;cytokine metabolic process;0.0289057852480629;21841!GO:0005634;nucleus;0.0289057852480629;21841,66867,18193!GO:0007369;gastrulation;0.0289057852480629;18193!GO:0006996;organelle organization and biogenesis;0.0291273914862101;66867,18193!GO:0051248;negative regulation of protein metabolic process;0.0305188836318489;21841!GO:0008757;S-adenosylmethionine-dependent methyltransferase activity;0.0308419047956447;18193!GO:0006730;one-carbon compound metabolic process;0.0333074784707566;18193!GO:0003682;chromatin binding;0.0412973269226017;18193!GO:0001816;cytokine production;0.0412973269226017;21841!
|gostat_on_MCL_coexpression=GO:0030331;estrogen receptor binding;0.00810825617706678;18193!GO:0046966;thyroid hormone receptor binding;0.00810825617706678;18193!GO:0046975;histone lysine N-methyltransferase activity (H3-K36 specific);0.00810825617706678;18193!GO:0016568;chromatin modification;0.00896215672069559;66867,18193!GO:0035258;steroid hormone receptor binding;0.00903808206770178;18193!GO:0042974;retinoic acid receptor binding;0.00903808206770178;18193!GO:0042799;histone lysine N-methyltransferase activity (H4-K20 specific);0.00903808206770178;18193!GO:0046965;retinoid X receptor binding;0.00903808206770178;18193!GO:0006325;establishment and/or maintenance of chromatin architecture;0.00903808206770178;66867,18193!GO:0017091;AU-rich element binding;0.00903808206770178;21841!GO:0006323;DNA packaging;0.00903808206770178;66867,18193!GO:0031324;negative regulation of cellular metabolic process;0.00933700986064206;21841,18193!GO:0016922;ligand-dependent nuclear receptor binding;0.00935362998129836;18193!GO:0009892;negative regulation of metabolic process;0.0102114007393278;21841,18193!GO:0051276;chromosome organization and biogenesis;0.0114543722633916;66867,18193!GO:0035097;histone methyltransferase complex;0.0114543722633916;18193!GO:0010468;regulation of gene expression;0.0114543722633916;21841,66867,18193!GO:0031323;regulation of cellular metabolic process;0.0122039355836149;21841,66867,18193!GO:0042036;negative regulation of cytokine biosynthetic process;0.0122478024990145;21841!GO:0019222;regulation of metabolic process;0.0122478024990145;21841,66867,18193!GO:0035257;nuclear hormone receptor binding;0.0127345656648945;18193!GO:0051427;hormone receptor binding;0.0132600607150388;18193!GO:0016571;histone methylation;0.0158518140714068;18193!GO:0018024;histone-lysine N-methyltransferase activity;0.0158907178865336;18193!GO:0016278;lysine N-methyltransferase activity;0.0158907178865336;18193!GO:0016279;protein-lysine N-methyltransferase activity;0.0158907178865336;18193!GO:0010467;gene expression;0.0168146204921224;21841,66867,18193!GO:0006259;DNA metabolic process;0.017233100952645;66867,18193!GO:0042054;histone methyltransferase activity;0.0198737457423813;18193!GO:0017148;negative regulation of translation;0.0198737457423813;21841!GO:0031327;negative regulation of cellular biosynthetic process;0.0198737457423813;21841!GO:0006479;protein amino acid methylation;0.0198737457423813;18193!GO:0008213;protein amino acid alkylation;0.0198737457423813;18193!GO:0001702;gastrulation with mouth forming second;0.0210871265304523;18193!GO:0050794;regulation of cellular process;0.0210871265304523;21841,66867,18193!GO:0009890;negative regulation of biosynthetic process;0.0210871265304523;21841!GO:0008170;N-methyltransferase activity;0.0210871265304523;18193!GO:0008276;protein methyltransferase activity;0.0210871265304523;18193!GO:0016570;histone modification;0.0211678896003258;18193!GO:0048523;negative regulation of cellular process;0.0216028946271842;21841,18193!GO:0016569;covalent chromatin modification;0.0219083509771772;18193!GO:0048519;negative regulation of biological process;0.0236369750219196;21841,18193!GO:0043414;biopolymer methylation;0.0236369750219196;18193!GO:0050789;regulation of biological process;0.0236369750219196;21841,66867,18193!GO:0032259;methylation;0.0242661749924914;18193!GO:0042035;regulation of cytokine biosynthetic process;0.026369046303537;21841!GO:0003714;transcription corepressor activity;0.0288954535041561;18193!GO:0065007;biological regulation;0.0289057852480629;21841,66867,18193!GO:0042089;cytokine biosynthetic process;0.0289057852480629;21841!GO:0042107;cytokine metabolic process;0.0289057852480629;21841!GO:0005634;nucleus;0.0289057852480629;21841,66867,18193!GO:0007369;gastrulation;0.0289057852480629;18193!GO:0006996;organelle organization and biogenesis;0.0291273914862101;66867,18193!GO:0051248;negative regulation of protein metabolic process;0.0305188836318489;21841!GO:0008757;S-adenosylmethionine-dependent methyltransferase activity;0.0308419047956447;18193!GO:0006730;one-carbon compound metabolic process;0.0333074784707566;18193!GO:0003682;chromatin binding;0.0412973269226017;18193!GO:0001816;cytokine production;0.0412973269226017;21841!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000153!7.44e-08!43;UBERON:0000468!5.64e-07!333
}}
}}

Revision as of 19:08, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr13:55313414..55313447,+p2@Nsd1
Mm9::chr6:86354251..86354313,+p1@Tia1
Mm9::chr9:56266612..56266654,+p1@Hmg20a


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:0030331estrogen receptor binding0.00810825617706678
GO:0046966thyroid hormone receptor binding0.00810825617706678
GO:0046975histone lysine N-methyltransferase activity (H3-K36 specific)0.00810825617706678
GO:0016568chromatin modification0.00896215672069559
GO:0035258steroid hormone receptor binding0.00903808206770178
GO:0042974retinoic acid receptor binding0.00903808206770178
GO:0042799histone lysine N-methyltransferase activity (H4-K20 specific)0.00903808206770178
GO:0046965retinoid X receptor binding0.00903808206770178
GO:0006325establishment and/or maintenance of chromatin architecture0.00903808206770178
GO:0017091AU-rich element binding0.00903808206770178
GO:0006323DNA packaging0.00903808206770178
GO:0031324negative regulation of cellular metabolic process0.00933700986064206
GO:0016922ligand-dependent nuclear receptor binding0.00935362998129836
GO:0009892negative regulation of metabolic process0.0102114007393278
GO:0051276chromosome organization and biogenesis0.0114543722633916
GO:0035097histone methyltransferase complex0.0114543722633916
GO:0010468regulation of gene expression0.0114543722633916
GO:0031323regulation of cellular metabolic process0.0122039355836149
GO:0042036negative regulation of cytokine biosynthetic process0.0122478024990145
GO:0019222regulation of metabolic process0.0122478024990145
GO:0035257nuclear hormone receptor binding0.0127345656648945
GO:0051427hormone receptor binding0.0132600607150388
GO:0016571histone methylation0.0158518140714068
GO:0018024histone-lysine N-methyltransferase activity0.0158907178865336
GO:0016278lysine N-methyltransferase activity0.0158907178865336
GO:0016279protein-lysine N-methyltransferase activity0.0158907178865336
GO:0010467gene expression0.0168146204921224
GO:0006259DNA metabolic process0.017233100952645
GO:0042054histone methyltransferase activity0.0198737457423813
GO:0017148negative regulation of translation0.0198737457423813
GO:0031327negative regulation of cellular biosynthetic process0.0198737457423813
GO:0006479protein amino acid methylation0.0198737457423813
GO:0008213protein amino acid alkylation0.0198737457423813
GO:0001702gastrulation with mouth forming second0.0210871265304523
GO:0050794regulation of cellular process0.0210871265304523
GO:0009890negative regulation of biosynthetic process0.0210871265304523
GO:0008170N-methyltransferase activity0.0210871265304523
GO:0008276protein methyltransferase activity0.0210871265304523
GO:0016570histone modification0.0211678896003258
GO:0048523negative regulation of cellular process0.0216028946271842
GO:0016569covalent chromatin modification0.0219083509771772
GO:0048519negative regulation of biological process0.0236369750219196
GO:0043414biopolymer methylation0.0236369750219196
GO:0050789regulation of biological process0.0236369750219196
GO:0032259methylation0.0242661749924914
GO:0042035regulation of cytokine biosynthetic process0.026369046303537
GO:0003714transcription corepressor activity0.0288954535041561
GO:0065007biological regulation0.0289057852480629
GO:0042089cytokine biosynthetic process0.0289057852480629
GO:0042107cytokine metabolic process0.0289057852480629
GO:0005634nucleus0.0289057852480629
GO:0007369gastrulation0.0289057852480629
GO:0006996organelle organization and biogenesis0.0291273914862101
GO:0051248negative regulation of protein metabolic process0.0305188836318489
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0308419047956447
GO:0006730one-carbon compound metabolic process0.0333074784707566
GO:0003682chromatin binding0.0412973269226017
GO:0001816cytokine production0.0412973269226017



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
anterior region of body7.44e-0843
multi-cellular organism5.64e-07333


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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