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MCL coexpression mm9:466: Difference between revisions

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{{MCL_coexpression_mm9
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ucleic acid binding;0.00530572852107038;212276,104836,53621,65020,67039,56469,212880!GO:0016070;RNA metabolic process;0.00903518597931577;212276,53621,65020,67039,56469,212880!GO:0046914;transition metal ion binding;0.00903518597931577;212276,104836,53621,65020,68916,56469!GO:0010467;gene expression;0.0150623954367083;212276,53621,65020,67039,56469,212880!GO:0043283;biopolymer metabolic process;0.0150623954367083;212276,104836,53621,65020,67039,56469,212880!GO:0008270;zinc ion binding;0.0155505022672948;212276,104836,53621,65020,56469!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0155505022672948;212276,53621,65020,67039,56469,212880!GO:0006512;ubiquitin cycle;0.0155505022672948;104836,53621,56469!GO:0043169;cation binding;0.0186580699103838;212276,104836,53621,65020,68916,56469!GO:0046872;metal ion binding;0.0262872557322886;212276,104836,53621,65020,68916,56469!GO:0043167;ion binding;0.0267108832279013;212276,104836,53621,65020,68916,56469!GO:0043170;macromolecule metabolic process;0.036282835004813;212276,104836,53621,65020,67039,56469,212880!GO:0006397;mRNA processing;0.0417523094957805;67039,212880!GO:0030335;positive regulation of cell migration;0.0417523094957805;104836!GO:0007162;negative regulation of cell adhesion;0.0417523094957805;104836!GO:0016071;mRNA metabolic process;0.0417523094957805;67039,212880!GO:0006355;regulation of transcription, DNA-dependent;0.0417523094957805;212276,53621,65020,56469!GO:0051272;positive regulation of cell motility;0.0417523094957805;104836!GO:0040017;positive regulation of locomotion;0.0417523094957805;104836!GO:0006351;transcription, DNA-dependent;0.0417523094957805;212276,53621,65020,56469!GO:0032774;RNA biosynthetic process;0.0417523094957805;212276,53621,65020,56469!GO:0044238;primary metabolic process;0.0417523094957805;212276,104836,53621,65020,67039,56469,212880!GO:0044237;cellular metabolic process;0.0417523094957805;212276,104836,53621,65020,67039,56469,212880!GO:0045449;regulation of transcription;0.0417523094957805;212276,53621,65020,56469!GO:0051539;4 iron, 4 sulfur cluster binding;0.0417523094957805;68916!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0417523094957805;212276,53621,65020,56469!GO:0006350;transcription;0.0417523094957805;212276,53621,65020,56469!GO:0050794;regulation of cellular process;0.0417523094957805;212276,104836,53621,65020,56469!GO:0045807;positive regulation of endocytosis;0.0417523094957805;104836!GO:0016874;ligase activity;0.0417523094957805;104836,53621!GO:0010468;regulation of gene expression;0.0449082443095962;212276,53621,65020,56469!GO:0006396;RNA processing;0.0449082443095962;67039,212880!GO:0007259;JAK-STAT cascade;0.047240253790555;56469!GO:0031323;regulation of cellular metabolic process;0.047240253790555;212276,53621,65020,56469!|ontology_enrichment_celltype=CL:0000791!5.18e-07!9;CL:0000789!5.18e-07!9;CL:0002420!5.18e-07!9;CL:0002419!5.18e-07!9;CL:0000790!5.18e-07!9;CL:0000542!7.05e-07!13;CL:0000051!7.05e-07!13|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001048!2.76e-10!134;UBERON:0000153!4.32e-10!43;UBERON:0001004!1.92e-09!42;UBERON:0000065!3.95e-09!41;UBERON:0000077!1.20e-08!35;UBERON:0007811!1.51e-08!36;UBERON:0004177!1.55e-08!29;UBERON:0005057!1.55e-08!29;UBERON:0003408!1.22e-07!24;UBERON:0006562!1.37e-07!24;UBERON:0001557!1.37e-07!24;UBERON:0001042!1.37e-07!24;UBERON:0008814!1.37e-07!24;UBERON:0009145!1.37e-07!24;UBERON:0002370!2.49e-07!23;UBERON:0000974!2.49e-07!23;UBERON:0004807!2.49e-07!23;UBERON:0005058!2.49e-07!23;UBERON:0003351!2.49e-07!23;UBERON:0009113!2.49e-07!23;UBERON:0003295!2.49e-07!23;UBERON:0009722!2.49e-07!23;UBERON:0005562!2.49e-07!23;UBERON:0007690!2.49e-07!23|tfbs_overrepresentation_for_novel_motifs=1.05939,0.333671,0.510781,0.221468,0.325044,0.656813,0.823081,0.416085,0.439801,0.491359,0.742008,0.800764,1.1257,0.845901,0.351364,0,1.21249,0.094037,0.167127,0.183206,0.146132,0.659668,2.32122,0.663197,0.176763,0.338177,0.0402178,0.694761,1.29108,0.262034,0.669223,0.574932,0.0927567,0.133454,0.352136,0.178588,1.03008,0.292182,0.262298,0.221026,0.0962801,0.678575,0.100408,0.109711,0.343478,1.14933,0.41191,0.723497,0.166243,0.801551,0.467043,0.947989,0.466115,0.7073,0.723811,0.321095,0.133938,0.777175,0.338309,1.54323,0.556492,0.369066,0.469805,1.15721,0.880059,0.493315,0.854035,1.19441,0.552202,1.05011,0.478436,0.0523282,0.261967,0.755651,0.322986,0.867289,0.313869,0.401969,0.540754,0.890942,0.433876,1.24599,0.36783,0.177942,0.646739,0.658811,0.103037,0.262344,1.06898,1.35441,0.92132,1.56881,0.586758,0.102076,0.073664,0.231057,0.183077,0.589355,0.412133,1.00795,0.0875773,0.574674,0.690844,0.467576,0.466632,1.25818,0.52055,0.716149,0.463457,0.147333,0.185018,0.692526,0.149729,0.273484,0.928143,0.0952498,0.402998,0.637592,0.483885,0.0854853,0.760792,0.438354,0.900811,0.40118,0.980682,1.34331,0.311744,0.580495,0.852575,0.691852,0.67485,1.16056,0.824167,0.332514,0.949083,0.649617,0.196278,0.24296,0.901468,1.71991,1.32292,0.85857,0.349901,0.584599,1.16552,0.242215,0.414644,1.68046,0.575158,0.672242,0.110319,0.594031,0.708784,0.0677483,0.331737,0.786435,0.94989,0.370626,0.188342,0.570508,0.910663,1.5574,0.544546,0.539942,0.457889,0.325532,0.293289,0.293837,0.393099|tfbs_overrepresentation_jaspar=MA0003.1;0.492928,MA0004.1;0.631712,MA0006.1;0.701162,MA0007.1;0.210531,MA0009.1;0.599391,MA0014.1;0.549152,MA0017.1;0.387005,MA0019.1;0.434009,MA0024.1;1.3747,MA0025.1;0.819843,MA0027.1;2.21717,MA0028.1;3.80908,MA0029.1;0.53905,MA0030.1;0.545058,MA0031.1;0.512616,MA0038.1;0.33811,MA0040.1;0.611015,MA0041.1;0.166538,MA0042.1;0.15744,MA0043.1;0.689898,MA0046.1;0.632833,MA0048.1;0.420794,MA0050.1;0.251816,MA0051.1;0.345658,MA0052.1;0.618515,MA0055.1;0.0114678,MA0056.1;0,MA0057.1;0.630217,MA0058.1;1.45452,MA0059.1;0.161227,MA0060.1;0.223836,MA0061.1;0.267107,MA0063.1;0,MA0066.1;0.328887,MA0067.1;0.92691,MA0068.1;0.650068,MA0069.1;0.618831,MA0070.1;0.609808,MA0071.1;0.251158,MA0072.1;0.601934,MA0073.1;1.30874e-05,MA0074.1;0.299171,MA0076.1;3.34757,MA0077.1;0.581866,MA0078.1;0.37382,MA0081.1;1.00846,MA0083.1;0.68915,MA0084.1;1.24749,MA0087.1;0.648637,MA0088.1;3.06757,MA0089.1;0,MA0090.1;0.196267,MA0091.1;0.231874,MA0092.1;0.196497,MA0093.1;1.23271,MA0095.1;0,MA0098.1;0,MA0100.1;0.289731,MA0101.1;0.167439,MA0103.1;0.128989,MA0105.1;0.556586,MA0106.1;0.380511,MA0107.1;0.394565,MA0108.2;0.454274,MA0109.1;0,MA0111.1;0.206727,MA0113.1;0.937714,MA0114.1;0.263654,MA0115.1;0.692537,MA0116.1;0.344035,MA0117.1;0.662171,MA0119.1;0.16785,MA0122.1;0.680832,MA0124.1;0.875485,MA0125.1;0.804312,MA0130.1;0,MA0131.1;1.09893,MA0132.1;0,MA0133.1;0,MA0135.1;0.724328,MA0136.1;0.315568,MA0139.1;0.406429,MA0140.1;0.289637,MA0141.1;0.141822,MA0142.1;0.499475,MA0143.1;0.37032,MA0144.1;0.95924,MA0145.1;0.277688,MA0146.1;0.320247,MA0147.1;0.599447,MA0148.1;0.23425,MA0149.1;0.171305,MA0062.2;4.72415,MA0035.2;0.293466,MA0039.2;0.989198,MA0138.2;0.423003,MA0002.2;0.185031,MA0137.2;1.3762,MA0104.2;0.204256,MA0047.2;0.337465,MA0112.2;0.277674,MA0065.2;0.136177,MA0150.1;0.210447,MA0151.1;0,MA0152.1;0.337555,MA0153.1;0.740107,MA0154.1;0.215016,MA0155.1;0.0605786,MA0156.1;0.826041,MA0157.1;0.47062,MA0158.1;0,MA0159.1;0.0900717,MA0160.1;0.23657,MA0161.1;0,MA0162.1;0.387966,MA0163.1;0.216701,MA0164.1;0.315868,MA0080.2;0.396013,MA0018.2;0.323932,MA0099.2;0.417463,MA0079.2;0.0421666,MA0102.2;1.29919,MA0258.1;0.522754,MA0259.1;0.270549,MA0442.1;0}}
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|gostat_on_MCL_coexpression=GO:0003676;nucleic acid binding;0.00530572852107038;212276,104836,53621,65020,67039,56469,212880!GO:0016070;RNA metabolic process;0.00903518597931577;212276,53621,65020,67039,56469,212880!GO:0046914;transition metal ion binding;0.00903518597931577;212276,104836,53621,65020,68916,56469!GO:0010467;gene expression;0.0150623954367083;212276,53621,65020,67039,56469,212880!GO:0043283;biopolymer metabolic process;0.0150623954367083;212276,104836,53621,65020,67039,56469,212880!GO:0008270;zinc ion binding;0.0155505022672948;212276,104836,53621,65020,56469!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0155505022672948;212276,53621,65020,67039,56469,212880!GO:0006512;ubiquitin cycle;0.0155505022672948;104836,53621,56469!GO:0043169;cation binding;0.0186580699103838;212276,104836,53621,65020,68916,56469!GO:0046872;metal ion binding;0.0262872557322886;212276,104836,53621,65020,68916,56469!GO:0043167;ion binding;0.0267108832279013;212276,104836,53621,65020,68916,56469!GO:0043170;macromolecule metabolic process;0.036282835004813;212276,104836,53621,65020,67039,56469,212880!GO:0006397;mRNA processing;0.0417523094957805;67039,212880!GO:0030335;positive regulation of cell migration;0.0417523094957805;104836!GO:0007162;negative regulation of cell adhesion;0.0417523094957805;104836!GO:0016071;mRNA metabolic process;0.0417523094957805;67039,212880!GO:0006355;regulation of transcription, DNA-dependent;0.0417523094957805;212276,53621,65020,56469!GO:0051272;positive regulation of cell motility;0.0417523094957805;104836!GO:0040017;positive regulation of locomotion;0.0417523094957805;104836!GO:0006351;transcription, DNA-dependent;0.0417523094957805;212276,53621,65020,56469!GO:0032774;RNA biosynthetic process;0.0417523094957805;212276,53621,65020,56469!GO:0044238;primary metabolic process;0.0417523094957805;212276,104836,53621,65020,67039,56469,212880!GO:0044237;cellular metabolic process;0.0417523094957805;212276,104836,53621,65020,67039,56469,212880!GO:0045449;regulation of transcription;0.0417523094957805;212276,53621,65020,56469!GO:0051539;4 iron, 4 sulfur cluster binding;0.0417523094957805;68916!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0417523094957805;212276,53621,65020,56469!GO:0006350;transcription;0.0417523094957805;212276,53621,65020,56469!GO:0050794;regulation of cellular process;0.0417523094957805;212276,104836,53621,65020,56469!GO:0045807;positive regulation of endocytosis;0.0417523094957805;104836!GO:0016874;ligase activity;0.0417523094957805;104836,53621!GO:0010468;regulation of gene expression;0.0449082443095962;212276,53621,65020,56469!GO:0006396;RNA processing;0.0449082443095962;67039,212880!GO:0007259;JAK-STAT cascade;0.047240253790555;56469!GO:0031323;regulation of cellular metabolic process;0.047240253790555;212276,53621,65020,56469!
}}

Latest revision as of 15:21, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:32184406..32184428,-p1@Cbll1
Mm9::chr12:70458107..70458168,-p1@Nemf
Mm9::chr12:84973158..84973275,+p1@Rbm25
Mm9::chr13:29947499..29947545,-p1@Cdkal1
Mm9::chr13:55736363..55736397,+p1@Ddx46
Mm9::chr13:67654035..67654112,-p1@Zfp748
Mm9::chr16:87432729..87432793,-p1@Ltn1
Mm9::chr3:51219908..51219966,+p1@Naa15
Mm9::chr4:132194943..132195033,+p1@Eya3
Mm9::chr4:48486275..48486329,-p1@Tex10
Mm9::chr5:124199383..124199400,-p1@Rsrc2
Mm9::chr5:151468135..151468181,-p1@N4bp2l2
Mm9::chr6:118369406..118369459,-p1@Bms1
Mm9::chr6:35083688..35083730,-p1@Cnot4
Mm9::chr7:13420322..13420401,+p1@Zfp110
Mm9::chr9:62828681..62828709,-p1@Pias1


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:0003676nucleic acid binding0.00530572852107038
GO:0016070RNA metabolic process0.00903518597931577
GO:0046914transition metal ion binding0.00903518597931577
GO:0010467gene expression0.0150623954367083
GO:0043283biopolymer metabolic process0.0150623954367083
GO:0008270zinc ion binding0.0155505022672948
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0155505022672948
GO:0006512ubiquitin cycle0.0155505022672948
GO:0043169cation binding0.0186580699103838
GO:0046872metal ion binding0.0262872557322886
GO:0043167ion binding0.0267108832279013
GO:0043170macromolecule metabolic process0.036282835004813
GO:0006397mRNA processing0.0417523094957805
GO:0030335positive regulation of cell migration0.0417523094957805
GO:0007162negative regulation of cell adhesion0.0417523094957805
GO:0016071mRNA metabolic process0.0417523094957805
GO:0006355regulation of transcription, DNA-dependent0.0417523094957805
GO:0051272positive regulation of cell motility0.0417523094957805
GO:0040017positive regulation of locomotion0.0417523094957805
GO:0006351transcription, DNA-dependent0.0417523094957805
GO:0032774RNA biosynthetic process0.0417523094957805
GO:0044238primary metabolic process0.0417523094957805
GO:0044237cellular metabolic process0.0417523094957805
GO:0045449regulation of transcription0.0417523094957805
GO:00515394 iron, 4 sulfur cluster binding0.0417523094957805
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0417523094957805
GO:0006350transcription0.0417523094957805
GO:0050794regulation of cellular process0.0417523094957805
GO:0045807positive regulation of endocytosis0.0417523094957805
GO:0016874ligase activity0.0417523094957805
GO:0010468regulation of gene expression0.0449082443095962
GO:0006396RNA processing0.0449082443095962
GO:0007259JAK-STAT cascade0.047240253790555
GO:0031323regulation of cellular metabolic process0.047240253790555



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
mature alpha-beta T cell5.18e-079
alpha-beta T cell5.18e-079
immature T cell5.18e-079
mature T cell5.18e-079
immature alpha-beta T cell5.18e-079
lymphocyte7.05e-0713
common lymphoid progenitor7.05e-0713


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)
MA0003.10.492928
MA0004.10.631712
MA0006.10.701162
MA0007.10.210531
MA0009.10.599391
MA0014.10.549152
MA0017.10.387005
MA0019.10.434009
MA0024.11.3747
MA0025.10.819843
MA0027.12.21717
MA0028.13.80908
MA0029.10.53905
MA0030.10.545058
MA0031.10.512616
MA0038.10.33811
MA0040.10.611015
MA0041.10.166538
MA0042.10.15744
MA0043.10.689898
MA0046.10.632833
MA0048.10.420794
MA0050.10.251816
MA0051.10.345658
MA0052.10.618515
MA0055.10.0114678
MA0056.10
MA0057.10.630217
MA0058.11.45452
MA0059.10.161227
MA0060.10.223836
MA0061.10.267107
MA0063.10
MA0066.10.328887
MA0067.10.92691
MA0068.10.650068
MA0069.10.618831
MA0070.10.609808
MA0071.10.251158
MA0072.10.601934
MA0073.11.30874e-05
MA0074.10.299171
MA0076.13.34757
MA0077.10.581866
MA0078.10.37382
MA0081.11.00846
MA0083.10.68915
MA0084.11.24749
MA0087.10.648637
MA0088.13.06757
MA0089.10
MA0090.10.196267
MA0091.10.231874
MA0092.10.196497
MA0093.11.23271
MA0095.10
MA0098.10
MA0100.10.289731
MA0101.10.167439
MA0103.10.128989
MA0105.10.556586
MA0106.10.380511
MA0107.10.394565
MA0108.20.454274
MA0109.10
MA0111.10.206727
MA0113.10.937714
MA0114.10.263654
MA0115.10.692537
MA0116.10.344035
MA0117.10.662171
MA0119.10.16785
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.11.09893
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.10.315568
MA0139.10.406429
MA0140.10.289637
MA0141.10.141822
MA0142.10.499475
MA0143.10.37032
MA0144.10.95924
MA0145.10.277688
MA0146.10.320247
MA0147.10.599447
MA0148.10.23425
MA0149.10.171305
MA0062.24.72415
MA0035.20.293466
MA0039.20.989198
MA0138.20.423003
MA0002.20.185031
MA0137.21.3762
MA0104.20.204256
MA0047.20.337465
MA0112.20.277674
MA0065.20.136177
MA0150.10.210447
MA0151.10
MA0152.10.337555
MA0153.10.740107
MA0154.10.215016
MA0155.10.0605786
MA0156.10.826041
MA0157.10.47062
MA0158.10
MA0159.10.0900717
MA0160.10.23657
MA0161.10
MA0162.10.387966
MA0163.10.216701
MA0164.10.315868
MA0080.20.396013
MA0018.20.323932
MA0099.20.417463
MA0079.20.0421666
MA0102.21.29919
MA0258.10.522754
MA0259.10.270549
MA0442.10
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