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MCL coexpression mm9:1188: Difference between revisions

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{{MCL_coexpression_mm9
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fibril organization;0.0296305349173371;16917!GO:0021954;central nervous system neuron development;0.0296305349173371;16917!GO:0021953;central nervous system neuron differentiation;0.0296305349173371;16917!GO:0009953;dorsal/ventral pattern formation;0.0296305349173371;16917!GO:0001764;neuron migration;0.0296305349173371;16917!GO:0030198;extracellular matrix organization and biogenesis;0.0296305349173371;16917!GO:0030326;embryonic limb morphogenesis;0.0296305349173371;16917!GO:0035113;embryonic appendage morphogenesis;0.0296305349173371;16917!GO:0043010;camera-type eye development;0.0296305349173371;16917!GO:0035107;appendage morphogenesis;0.0296305349173371;16917!GO:0035108;limb morphogenesis;0.0296305349173371;16917!GO:0048736;appendage development;0.0296305349173371;16917!GO:0060173;limb development;0.0296305349173371;16917!GO:0043062;extracellular structure organization and biogenesis;0.0338063149436622;16917!GO:0001654;eye development;0.0338063149436622;16917!GO:0003002;regionalization;0.0447974305593601;16917!|ontology_enrichment_celltype=CL:0000117!1.45e-10!23;CL:0000337!1.45e-10!23|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000970!1.74e-10!9;UBERON:0000019!1.74e-10!9;UBERON:0000047!1.74e-10!9;UBERON:0010312!1.74e-10!9;UBERON:0004088!1.74e-10!9;UBERON:0002104!1.74e-10!9;UBERON:0001456!1.74e-10!9;UBERON:0003072!1.74e-10!9;UBERON:0004128!1.74e-10!9;UBERON:0003071!1.74e-10!9;UBERON:0002102!5.07e-10!7;UBERON:0004710!5.07e-10!7;UBERON:0005419!5.07e-10!7;UBERON:0005417!5.07e-10!7;UBERON:0005729!5.07e-10!7;UBERON:0010708!1.58e-08!8;UBERON:0002240!3.08e-08!6;UBERON:0005174!3.08e-08!6;UBERON:0001137!3.08e-08!6;UBERON:0001444!3.95e-08!11;UBERON:0002346!1.95e-07!64;UBERON:0003075!1.95e-07!64;UBERON:0007284!1.95e-07!64;UBERON:0001948!2.91e-07!5;UBERON:0002315!2.91e-07!5;UBERON:0000020!2.97e-07!12;UBERON:0001032!2.97e-07!12;UBERON:0004456!2.97e-07!12|tfbs_overrepresentation_for_novel_motifs=1.11639,1.45672,0.411716,0.480627,0.299217,0.495263,0.587291,1.12275,0.616096,0.219671,0.542749,0.575086,0.59526,1.46059,0.315771,0,0.795315,0.291368,0.19222,1.75604,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,1.0368,0.516511,0.344372,0.145661,0.50223,0.897561,0.289148,0.498917,0.316253,1.10671,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.0742755,0.317766,0.822425,2.05905,0.714592,0.532496,0.0609361,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,1.3814,0.176152,0.604914,0.877332,1.59614,1.20126,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,1.52206,1.09164,0.507615,2.14449,0.166511,0.703064,0.859987,0.378988,1.14907,0.812889,0.663039,0.200155,0.975495,0.613286,0.667407,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.823238,0.254625,0.237542,0.203879,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.187586,3.12145,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,2.00769,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,2.74845,0.545091,1.04192,0.681896,0.619892,1.12411,0.655955,0.327731,0.435579,1.13413,1.25393,0.974632,0.864173,1.92222,0.767269,0.612377,0.278874,0.573477,0.227149|tfbs_overrepresentation_jaspar=MA0003.1;10.091,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;4.64523,MA0017.1;1.60852,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;1.30252,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.648475,MA0056.1;0,MA0057.1;3.14169,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;1.22438,MA0061.1;0.724575,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;2.47843,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;3.21178,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.285759,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;4.5223,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;3.82007,MA0116.1;0.311187,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;1.46167,MA0139.1;0.585936,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.72625,MA0145.1;1.56174,MA0146.1;3.11443,MA0147.1;0.753844,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;4.97531,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.624968,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;1.0577,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.397336,MA0155.1;1.13804,MA0156.1;2.52393,MA0157.1;0.781683,MA0158.1;0,MA0159.1;2.17158,MA0160.1;0.50056,MA0161.1;0,MA0162.1;4.62777,MA0163.1;3.21163,MA0164.1;0.600609,MA0080.2;1.62792,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;13.7759,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0}}
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|gostat_on_MCL_coexpression=GO:0030199;collagen fibril organization;0.0296305349173371;16917!GO:0021954;central nervous system neuron development;0.0296305349173371;16917!GO:0021953;central nervous system neuron differentiation;0.0296305349173371;16917!GO:0009953;dorsal/ventral pattern formation;0.0296305349173371;16917!GO:0001764;neuron migration;0.0296305349173371;16917!GO:0030198;extracellular matrix organization and biogenesis;0.0296305349173371;16917!GO:0030326;embryonic limb morphogenesis;0.0296305349173371;16917!GO:0035113;embryonic appendage morphogenesis;0.0296305349173371;16917!GO:0043010;camera-type eye development;0.0296305349173371;16917!GO:0035107;appendage morphogenesis;0.0296305349173371;16917!GO:0035108;limb morphogenesis;0.0296305349173371;16917!GO:0048736;appendage development;0.0296305349173371;16917!GO:0060173;limb development;0.0296305349173371;16917!GO:0043062;extracellular structure organization and biogenesis;0.0338063149436622;16917!GO:0001654;eye development;0.0338063149436622;16917!GO:0003002;regionalization;0.0447974305593601;16917!
}}

Latest revision as of 16:32, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:33496386..33496410,-p1@Lmx1b
Mm9::chr2:33496574..33496588,+p4@ENSMUST00000152118
p4@uc008jhz.1
Mm9::chr2:33496584..33496601,-p@chr2:33496584..33496601
-
Mm9::chr2:33496770..33496783,+p1@ENSMUST00000152118
p1@uc008jhz.1
Mm9::chr2:33496787..33496842,+p1@ENSMUST00000147294
p1@uc008jia.1
Mm9::chr2:33496847..33496857,+p3@ENSMUST00000147294
p3@uc008jia.1
Mm9::chr2:33498116..33498124,+p@chr2:33498116..33498124
+


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:0030199collagen fibril organization0.0296305349173371
GO:0021954central nervous system neuron development0.0296305349173371
GO:0021953central nervous system neuron differentiation0.0296305349173371
GO:0009953dorsal/ventral pattern formation0.0296305349173371
GO:0001764neuron migration0.0296305349173371
GO:0030198extracellular matrix organization and biogenesis0.0296305349173371
GO:0030326embryonic limb morphogenesis0.0296305349173371
GO:0035113embryonic appendage morphogenesis0.0296305349173371
GO:0043010camera-type eye development0.0296305349173371
GO:0035107appendage morphogenesis0.0296305349173371
GO:0035108limb morphogenesis0.0296305349173371
GO:0048736appendage development0.0296305349173371
GO:0060173limb development0.0296305349173371
GO:0043062extracellular structure organization and biogenesis0.0338063149436622
GO:0001654eye development0.0338063149436622
GO:0003002regionalization0.0447974305593601



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
CNS neuron (sensu Vertebrata)1.45e-1023
neuroblast (sensu Vertebrata)1.45e-1023

Uber Anatomy
Ontology termp-valuen
eye1.74e-109
camera-type eye1.74e-109
simple eye1.74e-109
immature eye1.74e-109
ocular region1.74e-109
visual system1.74e-109
face1.74e-109
optic cup1.74e-109
optic vesicle1.74e-109
eye primordium1.74e-109
forelimb5.07e-107
pectoral appendage5.07e-107
pectoral appendage bud5.07e-107
forelimb bud5.07e-107
forelimb/pectoral fin field5.07e-107
pectoral complex1.58e-088
spinal cord3.08e-086
dorsal region element3.08e-086
dorsum3.08e-086
subdivision of head3.95e-0811
neurectoderm1.95e-0764
neural plate1.95e-0764
presumptive neural plate1.95e-0764
regional part of spinal cord2.91e-075
gray matter of spinal cord2.91e-075
sense organ2.97e-0712
sensory system2.97e-0712
entire sense organ system2.97e-0712


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)
MA0003.110.091
MA0004.10.481116
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.14.64523
MA0017.11.60852
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
MA0048.11.30252
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.648475
MA0056.10
MA0057.13.14169
MA0058.10.384683
MA0059.10.397033
MA0060.11.22438
MA0061.10.724575
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.12.47843
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.13.21178
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.14.5223
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.13.82007
MA0116.10.311187
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
MA0136.11.46167
MA0139.10.585936
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.72625
MA0145.11.56174
MA0146.13.11443
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.24.97531
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.0910939
MA0065.21.0577
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.11.13804
MA0156.12.52393
MA0157.10.781683
MA0158.10
MA0159.12.17158
MA0160.10.50056
MA0161.10
MA0162.14.62777
MA0163.13.21163
MA0164.10.600609
MA0080.21.62792
MA0018.20.610433
MA0099.20.721008
MA0079.213.7759
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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