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MCL coexpression mm9:912: Difference between revisions

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{{MCL_coexpression_mm9
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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 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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!
|ontology_enrichment_celltype=CL:0000540!2.82e-09!33;CL:0000047!2.82e-09!33;CL:0000031!2.82e-09!33;CL:0000404!2.82e-09!33;CL:0000221!3.12e-07!44;CL:0000133!3.12e-07!44;CL:0002319!4.13e-07!43;CL:0000117!7.72e-07!23;CL:0000337!7.72e-07!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!6.61e-07!64;UBERON:0003075!6.61e-07!64;UBERON:0007284!6.61e-07!64;UBERON:0001017!7.09e-07!73;UBERON:0001016!9.72e-07!75
}}

Latest revision as of 16:05, 17 September 2013


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><br>

Cell Type
Ontology termp-valuen
neuron2.82e-0933
neuronal stem cell2.82e-0933
neuroblast2.82e-0933
electrically signaling cell2.82e-0933
ectodermal cell3.12e-0744
neurectodermal cell3.12e-0744
neural cell4.13e-0743
CNS neuron (sensu Vertebrata)7.72e-0723
neuroblast (sensu Vertebrata)7.72e-0723

Uber Anatomy
Ontology termp-valuen
neurectoderm6.61e-0764
neural plate6.61e-0764
presumptive neural plate6.61e-0764
central nervous system7.09e-0773
nervous system9.72e-0775


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)
MA0003.10.602903
MA0004.11.10905
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.10.829081
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.919611
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.0283571
MA0056.10
MA0057.11.58436
MA0058.10.341628
MA0059.10.353484
MA0060.13.21257
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.138438
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.11.43515
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.814533
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.747001
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.640537
MA0145.10.0701568
MA0146.10.636109
MA0147.11.92563
MA0148.10.450593
MA0149.10.367458
MA0062.20.426733
MA0035.20.524137
MA0039.20.402847
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.21.64215
MA0047.20.576767
MA0112.20.2464
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.579465
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.11.05113
MA0163.10.408151
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.22.62627
MA0102.21.59466
MA0258.10.210437
MA0259.11.2032
MA0442.10
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