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MCL coexpression mm9:2828: Difference between revisions

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{{MCL_coexpression_mm9
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of macrophage activation;0.0119513702105763;19883!GO:0042116;macrophage activation;0.0119513702105763;19883!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.0119513702105763;19883!GO:0021694;cerebellar Purkinje cell layer formation;0.0119513702105763;19883!GO:0021702;cerebellar Purkinje cell differentiation;0.0119513702105763;19883!GO:0021697;cerebellar cortex formation;0.0119513702105763;19883!GO:0021533;cell differentiation in hindbrain;0.0119513702105763;19883!GO:0021680;cerebellar Purkinje cell layer development;0.0119513702105763;19883!GO:0021696;cerebellar cortex morphogenesis;0.0119513702105763;19883!GO:0046068;cGMP metabolic process;0.0119513702105763;19883!GO:0021587;cerebellum morphogenesis;0.0119513702105763;19883!GO:0021575;hindbrain morphogenesis;0.0119513702105763;19883!GO:0046209;nitric oxide metabolic process;0.0119513702105763;19883!GO:0006809;nitric oxide biosynthetic process;0.0119513702105763;19883!GO:0003700;transcription factor activity;0.0119513702105763;19883,432731!GO:0021695;cerebellar cortex development;0.0119513702105763;19883!GO:0022037;metencephalon development;0.0135725356259295;19883!GO:0021549;cerebellum development;0.0135725356259295;19883!GO:0002274;myeloid leukocyte activation;0.0150927438914705;19883!GO:0009187;cyclic nucleotide metabolic process;0.0196431301828096;19883!GO:0030902;hindbrain development;0.0212329048452931;19883!GO:0003707;steroid hormone receptor activity;0.0221524288309846;19883!GO:0004879;ligand-dependent nuclear receptor activity;0.0221524288309846;19883!GO:0044271;nitrogen compound biosynthetic process;0.0329664885539245;19883!GO:0050865;regulation of cell activation;0.0329664885539245;19883!GO:0006355;regulation of transcription, DNA-dependent;0.0329664885539245;19883,432731!GO:0006351;transcription, DNA-dependent;0.0329664885539245;19883,432731!GO:0032774;RNA biosynthetic process;0.0329664885539245;19883,432731!GO:0008270;zinc ion binding;0.0329664885539245;19883,432731!GO:0003677;DNA binding;0.0329664885539245;19883,432731!GO:0045449;regulation of transcription;0.0329664885539245;19883,432731!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0330521262380725;19883,432731!GO:0006350;transcription;0.0330521262380725;19883,432731!GO:0010468;regulation of gene expression;0.0342708745815109;19883,432731!GO:0031323;regulation of cellular metabolic process;0.0360768799411129;19883,432731!GO:0019222;regulation of metabolic process;0.0377164590634241;19883,432731!GO:0016070;RNA metabolic process;0.0386599017045434;19883,432731!GO:0046914;transition metal ion binding;0.0396731863729357;19883,432731!GO:0009117;nucleotide metabolic process;0.0473294077360537;19883!GO:0007420;brain development;0.0473294077360537;19883!GO:0048646;anatomical structure formation;0.0473294077360537;19883!GO:0010467;gene expression;0.0473294077360537;19883,432731!GO:0055086;nucleobase, nucleoside 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|gostat_on_MCL_coexpression=GO:0043030;regulation of macrophage activation;0.0119513702105763;19883!GO:0042116;macrophage activation;0.0119513702105763;19883!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.0119513702105763;19883!GO:0021694;cerebellar Purkinje cell layer formation;0.0119513702105763;19883!GO:0021702;cerebellar Purkinje cell differentiation;0.0119513702105763;19883!GO:0021697;cerebellar cortex formation;0.0119513702105763;19883!GO:0021533;cell differentiation in hindbrain;0.0119513702105763;19883!GO:0021680;cerebellar Purkinje cell layer development;0.0119513702105763;19883!GO:0021696;cerebellar cortex morphogenesis;0.0119513702105763;19883!GO:0046068;cGMP metabolic process;0.0119513702105763;19883!GO:0021587;cerebellum morphogenesis;0.0119513702105763;19883!GO:0021575;hindbrain morphogenesis;0.0119513702105763;19883!GO:0046209;nitric oxide metabolic process;0.0119513702105763;19883!GO:0006809;nitric oxide biosynthetic process;0.0119513702105763;19883!GO:0003700;transcription factor activity;0.0119513702105763;19883,432731!GO:0021695;cerebellar cortex development;0.0119513702105763;19883!GO:0022037;metencephalon development;0.0135725356259295;19883!GO:0021549;cerebellum development;0.0135725356259295;19883!GO:0002274;myeloid leukocyte activation;0.0150927438914705;19883!GO:0009187;cyclic nucleotide metabolic process;0.0196431301828096;19883!GO:0030902;hindbrain development;0.0212329048452931;19883!GO:0003707;steroid hormone receptor activity;0.0221524288309846;19883!GO:0004879;ligand-dependent nuclear receptor activity;0.0221524288309846;19883!GO:0044271;nitrogen compound biosynthetic process;0.0329664885539245;19883!GO:0050865;regulation of cell activation;0.0329664885539245;19883!GO:0006355;regulation of transcription, DNA-dependent;0.0329664885539245;19883,432731!GO:0006351;transcription, DNA-dependent;0.0329664885539245;19883,432731!GO:0032774;RNA biosynthetic process;0.0329664885539245;19883,432731!GO:0008270;zinc ion binding;0.0329664885539245;19883,432731!GO:0003677;DNA binding;0.0329664885539245;19883,432731!GO:0045449;regulation of transcription;0.0329664885539245;19883,432731!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0330521262380725;19883,432731!GO:0006350;transcription;0.0330521262380725;19883,432731!GO:0010468;regulation of gene expression;0.0342708745815109;19883,432731!GO:0031323;regulation of cellular metabolic process;0.0360768799411129;19883,432731!GO:0019222;regulation of metabolic process;0.0377164590634241;19883,432731!GO:0016070;RNA metabolic process;0.0386599017045434;19883,432731!GO:0046914;transition metal ion binding;0.0396731863729357;19883,432731!GO:0009117;nucleotide metabolic process;0.0473294077360537;19883!GO:0007420;brain development;0.0473294077360537;19883!GO:0048646;anatomical structure formation;0.0473294077360537;19883!GO:0010467;gene expression;0.0473294077360537;19883,432731!GO:0055086;nucleobase, nucleoside and nucleotide metabolic process;0.0473294077360537;19883!GO:0045944;positive regulation of transcription from RNA polymerase II promoter;0.0473294077360537;19883!GO:0003676;nucleic acid binding;0.0473294077360537;19883,432731!GO:0045321;leukocyte activation;0.0473294077360537;19883!GO:0001775;cell activation;0.0496748534331398;19883!GO:0007417;central nervous system development;0.0499057757583858;19883!GO:0045893;positive regulation of transcription, DNA-dependent;0.0499057757583858;19883!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0499057757583858;19883,432731!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004111!1.56e-10!122;UBERON:0000025!4.08e-10!114;UBERON:0000468!4.15e-09!333;UBERON:0010314!4.94e-08!92;UBERON:0000479!2.28e-07!349
|tfbs_overrepresentation_for_novel_motifs=1.77936,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,2.0216,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,1.7585,0.825437,1.24901,0.575271,0.411696,0.608816,0.444545,1.38481,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.474221,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,1.6706,0.474956,5.97285,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,5.73457,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,2.77583,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,1.44008,0.38417,2.85884,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
}}

Latest revision as of 19:08, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:21545538..21545569,-p2@Zfp187
Mm9::chr9:68501549..68501564,+p6@Rora
Mm9::chr9:68501568..68501592,+p3@Rora


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:0043030regulation of macrophage activation0.0119513702105763
GO:0042116macrophage activation0.0119513702105763
GO:0021692cerebellar Purkinje cell layer morphogenesis0.0119513702105763
GO:0021694cerebellar Purkinje cell layer formation0.0119513702105763
GO:0021702cerebellar Purkinje cell differentiation0.0119513702105763
GO:0021697cerebellar cortex formation0.0119513702105763
GO:0021533cell differentiation in hindbrain0.0119513702105763
GO:0021680cerebellar Purkinje cell layer development0.0119513702105763
GO:0021696cerebellar cortex morphogenesis0.0119513702105763
GO:0046068cGMP metabolic process0.0119513702105763
GO:0021587cerebellum morphogenesis0.0119513702105763
GO:0021575hindbrain morphogenesis0.0119513702105763
GO:0046209nitric oxide metabolic process0.0119513702105763
GO:0006809nitric oxide biosynthetic process0.0119513702105763
GO:0003700transcription factor activity0.0119513702105763
GO:0021695cerebellar cortex development0.0119513702105763
GO:0022037metencephalon development0.0135725356259295
GO:0021549cerebellum development0.0135725356259295
GO:0002274myeloid leukocyte activation0.0150927438914705
GO:0009187cyclic nucleotide metabolic process0.0196431301828096
GO:0030902hindbrain development0.0212329048452931
GO:0003707steroid hormone receptor activity0.0221524288309846
GO:0004879ligand-dependent nuclear receptor activity0.0221524288309846
GO:0044271nitrogen compound biosynthetic process0.0329664885539245
GO:0050865regulation of cell activation0.0329664885539245
GO:0006355regulation of transcription, DNA-dependent0.0329664885539245
GO:0006351transcription, DNA-dependent0.0329664885539245
GO:0032774RNA biosynthetic process0.0329664885539245
GO:0008270zinc ion binding0.0329664885539245
GO:0003677DNA binding0.0329664885539245
GO:0045449regulation of transcription0.0329664885539245
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0330521262380725
GO:0006350transcription0.0330521262380725
GO:0010468regulation of gene expression0.0342708745815109
GO:0031323regulation of cellular metabolic process0.0360768799411129
GO:0019222regulation of metabolic process0.0377164590634241
GO:0016070RNA metabolic process0.0386599017045434
GO:0046914transition metal ion binding0.0396731863729357
GO:0009117nucleotide metabolic process0.0473294077360537
GO:0007420brain development0.0473294077360537
GO:0048646anatomical structure formation0.0473294077360537
GO:0010467gene expression0.0473294077360537
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0473294077360537
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0473294077360537
GO:0003676nucleic acid binding0.0473294077360537
GO:0045321leukocyte activation0.0473294077360537
GO:0001775cell activation0.0496748534331398
GO:0007417central nervous system development0.0499057757583858
GO:0045893positive regulation of transcription, DNA-dependent0.0499057757583858
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0499057757583858



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
anatomical conduit1.56e-10122
tube4.08e-10114
multi-cellular organism4.15e-09333
structure with developmental contribution from neural crest4.94e-0892
tissue2.28e-07349


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)
MA0003.10.245953
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.416365
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.11.06076
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.439282
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.0481552
MA0138.21.07027
MA0002.21.17677
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.964824
MA0163.10.927936
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.288542
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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