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MCL coexpression mm9:1096: Difference between revisions

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{{MCL_coexpression_mm9
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specification process;0.000153943056126016;15399,15402,103889!GO:0005667;transcription factor complex;0.000315835053414219;15399,15402,103889!GO:0043565;sequence-specific DNA binding;0.000315835053414219;15399,15402,103889!GO:0044451;nucleoplasm part;0.00039402010379568;15399,15402,103889!GO:0005654;nucleoplasm;0.00039402010379568;15399,15402,103889!GO:0031981;nuclear lumen;0.000551916113459114;15399,15402,103889!GO:0031974;membrane-enclosed lumen;0.000594239712410312;15399,15402,103889!GO:0043233;organelle lumen;0.000594239712410312;15399,15402,103889!GO:0003700;transcription factor activity;0.000700170475403781;15399,15402,103889!GO:0044428;nuclear part;0.00111763160844294;15399,15402,103889!GO:0001501;skeletal development;0.00193913542639484;15399,15402!GO:0048513;organ development;0.00234322078843713;15399,15402,103889!GO:0043234;protein complex;0.00347439578904433;15399,15402,103889!GO:0048703;embryonic viscerocranium morphogenesis;0.00347439578904433;15399!GO:0048731;system development;0.00352670701653998;15399,15402,103889!GO:0006355;regulation of transcription, DNA-dependent;0.00352698103268352;15399,15402,103889!GO:0048701;embryonic cranial skeleton morphogenesis;0.00352698103268352;15399!GO:0042474;middle ear morphogenesis;0.00352698103268352;15399!GO:0006351;transcription, DNA-dependent;0.00352698103268352;15399,15402,103889!GO:0032774;RNA biosynthetic process;0.00352698103268352;15399,15402,103889!GO:0003677;DNA binding;0.00352698103268352;15399,15402,103889!GO:0045449;regulation of transcription;0.00352698103268352;15399,15402,103889!GO:0048856;anatomical structure development;0.00352698103268352;15399,15402,103889!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00352698103268352;15399,15402,103889!GO:0006350;transcription;0.00352698103268352;15399,15402,103889!GO:0032991;macromolecular complex;0.00353528059212516;15399,15402,103889!GO:0010468;regulation of gene expression;0.00360600608291956;15399,15402,103889!GO:0031323;regulation of cellular metabolic process;0.00392269358044763;15399,15402,103889!GO:0007275;multicellular organismal development;0.00395090403194017;15399,15402,103889!GO:0030878;thyroid gland development;0.00395090403194017;15402!GO:0019222;regulation of metabolic process;0.00395090403194017;15399,15402,103889!GO:0016070;RNA metabolic process;0.0040519072570119;15399,15402,103889!GO:0048704;embryonic skeletal morphogenesis;0.0040519072570119;15399!GO:0044446;intracellular organelle part;0.00419771021870457;15399,15402,103889!GO:0044422;organelle part;0.00419771021870457;15399,15402,103889!GO:0009887;organ morphogenesis;0.00449832583067754;15399,103889!GO:0048706;embryonic skeletal development;0.00525508818876713;15399!GO:0010467;gene expression;0.00597361517483295;15399,15402,103889!GO:0003676;nucleic acid binding;0.00625208640842819;15399,15402,103889!GO:0032502;developmental process;0.00670053665632696;15399,15402,103889!GO:0048705;skeletal morphogenesis;0.0068145802385791;15399!GO:0001709;cell fate determination;0.00694117952400784;15399!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00709741175974999;15399,15402,103889!GO:0050794;regulation of cellular process;0.00855503059975862;15399,15402,103889!GO:0050789;regulation of biological process;0.0115558544551607;15399,15402,103889!GO:0035270;endocrine system development;0.0126585304750465;15402!GO:0065007;biological regulation;0.0147516341067968;15399,15402,103889!GO:0042471;ear morphogenesis;0.0147516341067968;15399!GO:0035264;multicellular organism growth;0.0147516341067968;15402!GO:0005634;nucleus;0.0147516341067968;15399,15402,103889!GO:0032501;multicellular organismal process;0.0147516341067968;15399,15402,103889!GO:0009653;anatomical structure morphogenesis;0.0151095004532011;15399,103889!GO:0043283;biopolymer metabolic 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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005178!1.34e-11!17;UBERON:0005181!1.34e-11!17;UBERON:0002224!1.34e-11!17;UBERON:0000915!1.34e-11!17;UBERON:0008947!1.34e-11!17;UBERON:0003258!1.34e-11!17;UBERON:0002048!6.50e-10!14;UBERON:0000117!6.50e-10!14;UBERON:0000171!6.50e-10!14;UBERON:0000170!6.50e-10!14;UBERON:0005597!6.50e-10!14;UBERON:0000118!6.50e-10!14;UBERON:0005157!3.00e-09!20;UBERON:0005153!5.08e-07!17;UBERON:0005177!7.76e-07!79
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.0609112,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.792229,0.19222,0.112498,0.374752,0.08187,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,0.344372,0.145661,1.25421,0.897561,0.289148,0.166577,0.848378,0.101236,1.40094,0.57142,0.717242,0.230656,0.295233,0.507468,0.258106,0.317766,0.0275764,0.469348,0.714592,1.31862,0.0609361,0.917701,1.83068,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,3.39997,1.09164,0.507615,0.159969,0.166511,0.703064,0.859987,0.378988,0.212973,1.90329,0.663039,0.580284,0.975495,0.960306,0.374181,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,1.11365,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.418498,0.484437,1.86983,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,2.09861,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,1.38961,1.04192,1.26486,0.619892,1.12411,0.655955,0.327731,1.11101,1.13413,1.25393,0.974632,0.864173,1.92222,0.767269,0.612377,0.763807,0.573477,0.227149
|tfbs_overrepresentation_jaspar=MA0003.1;0.54119,MA0004.1;1.20906,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.694761,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.648475,MA0056.1;0,MA0057.1;1.23731,MA0058.1;2.66057,MA0059.1;1.81442,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.385183,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;11.2967,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;7.11247,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.598004,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;1.58083,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.488671,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;1.0246,MA0116.1;0.836994,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;1.7399,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.0910975,MA0146.1;0.264322,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;1.37408,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.102995,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;2.75316,MA0163.1;5.85525,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;7.04343,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0
}}

Latest revision as of 16:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:96214200..96214214,+p@chr11:96214200..96214214
+
Mm9::chr6:52114821..52114828,-p1@Hoxa2
Mm9::chr6:52125954..52125994,-p@chr6:52125954..52125994
-
Mm9::chr6:52141617..52141644,-p@chr6:52141617..52141644
-
Mm9::chr6:52154314..52154337,-p@chr6:52154314..52154337
-
Mm9::chr6:52154386..52154407,-p2@Hoxa5
Mm9::chr6:52154414..52154462,-p1@Hoxa5


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:0007389pattern specification process0.000153943056126016
GO:0005667transcription factor complex0.000315835053414219
GO:0043565sequence-specific DNA binding0.000315835053414219
GO:0044451nucleoplasm part0.00039402010379568
GO:0005654nucleoplasm0.00039402010379568
GO:0031981nuclear lumen0.000551916113459114
GO:0031974membrane-enclosed lumen0.000594239712410312
GO:0043233organelle lumen0.000594239712410312
GO:0003700transcription factor activity0.000700170475403781
GO:0044428nuclear part0.00111763160844294
GO:0001501skeletal development0.00193913542639484
GO:0048513organ development0.00234322078843713
GO:0043234protein complex0.00347439578904433
GO:0048703embryonic viscerocranium morphogenesis0.00347439578904433
GO:0048731system development0.00352670701653998
GO:0006355regulation of transcription, DNA-dependent0.00352698103268352
GO:0048701embryonic cranial skeleton morphogenesis0.00352698103268352
GO:0042474middle ear morphogenesis0.00352698103268352
GO:0006351transcription, DNA-dependent0.00352698103268352
GO:0032774RNA biosynthetic process0.00352698103268352
GO:0003677DNA binding0.00352698103268352
GO:0045449regulation of transcription0.00352698103268352
GO:0048856anatomical structure development0.00352698103268352
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00352698103268352
GO:0006350transcription0.00352698103268352
GO:0032991macromolecular complex0.00353528059212516
GO:0010468regulation of gene expression0.00360600608291956
GO:0031323regulation of cellular metabolic process0.00392269358044763
GO:0007275multicellular organismal development0.00395090403194017
GO:0030878thyroid gland development0.00395090403194017
GO:0019222regulation of metabolic process0.00395090403194017
GO:0016070RNA metabolic process0.0040519072570119
GO:0048704embryonic skeletal morphogenesis0.0040519072570119
GO:0044446intracellular organelle part0.00419771021870457
GO:0044422organelle part0.00419771021870457
GO:0009887organ morphogenesis0.00449832583067754
GO:0048706embryonic skeletal development0.00525508818876713
GO:0010467gene expression0.00597361517483295
GO:0003676nucleic acid binding0.00625208640842819
GO:0032502developmental process0.00670053665632696
GO:0048705skeletal morphogenesis0.0068145802385791
GO:0001709cell fate determination0.00694117952400784
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00709741175974999
GO:0050794regulation of cellular process0.00855503059975862
GO:0050789regulation of biological process0.0115558544551607
GO:0035270endocrine system development0.0126585304750465
GO:0065007biological regulation0.0147516341067968
GO:0042471ear morphogenesis0.0147516341067968
GO:0035264multicellular organism growth0.0147516341067968
GO:0005634nucleus0.0147516341067968
GO:0032501multicellular organismal process0.0147516341067968
GO:0009653anatomical structure morphogenesis0.0151095004532011
GO:0043283biopolymer metabolic process0.0152994450375327
GO:0048732gland development0.0166003981102075
GO:0043583ear development0.016737238024913
GO:0045165cell fate commitment0.0216009514315933
GO:0043170macromolecule metabolic process0.0322573700262882
GO:0007423sensory organ development0.0386095019991401
GO:0048598embryonic morphogenesis0.040982185860779
GO:0043009chordate embryonic development0.0441184110103377
GO:0009792embryonic development ending in birth or egg hatching0.0441184110103377
GO:0044238primary metabolic process0.0448612696373388
GO:0044237cellular metabolic process0.0448612696373388
GO:0043231intracellular membrane-bound organelle0.0448612696373388
GO:0043227membrane-bound organelle0.0448612696373388



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
thoracic cavity element1.34e-1117
thoracic segment organ1.34e-1117
thoracic cavity1.34e-1117
thoracic segment of trunk1.34e-1117
respiratory primordium1.34e-1117
endoderm of foregut1.34e-1117
lung6.50e-1014
respiratory tube6.50e-1014
respiration organ6.50e-1014
pair of lungs6.50e-1014
lung primordium6.50e-1014
lung bud6.50e-1014
epithelial fold3.00e-0920
epithelial bud5.08e-0717
trunk region element7.76e-0779


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)
MA0003.10.54119
MA0004.11.20906
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.694761
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.648475
MA0056.10
MA0057.11.23731
MA0058.12.66057
MA0059.11.81442
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.111.2967
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.17.11247
MA0084.11.59945
MA0087.10.977537
MA0088.10.598004
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.11.58083
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.488671
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.836994
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.11.7399
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.10.264322
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.21.37408
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.102995
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.12.75316
MA0163.15.85525
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.27.04343
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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