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MCL coexpression mm9:1069: Difference between revisions

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{{MCL_coexpression_mm9
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ossification;0.00753218282791926;14172!GO:0002063;chondrocyte development;0.00753218282791926;14172!GO:0030949;positive regulation of vascular endothelial growth factor receptor signaling pathway;0.00753218282791926;14172!GO:0030947;regulation of vascular endothelial growth factor receptor signaling pathway;0.00753218282791926;14172!GO:0001958;endochondral ossification;0.00964040159283091;14172!GO:0048010;vascular endothelial growth factor receptor signaling pathway;0.0129087757991752;14172!GO:0002062;chondrocyte differentiation;0.0129087757991752;14172!GO:0005104;fibroblast growth factor receptor binding;0.014305658165835;14172!GO:0051216;cartilage development;0.0320994530025149;14172!GO:0030324;lung development;0.0325858050159078;14172!GO:0009967;positive regulation of signal transduction;0.0325858050159078;14172!GO:0030323;respiratory tube development;0.0325858050159078;14172!GO:0001503;ossification;0.0403599296141723;14172!GO:0031214;biomineral formation;0.0403599296141723;14172!GO:0046849;bone remodeling;0.0412656971515578;14172!GO:0048771;tissue remodeling;0.0454248818374421;14172!GO:0001525;angiogenesis;0.0474795406709817;14172!GO:0008083;growth factor activity;0.0474795406709817;14172!GO:0007169;transmembrane receptor protein tyrosine kinase signaling pathway;0.0474795406709817;14172!GO:0048514;blood vessel morphogenesis;0.0474795406709817;14172!GO:0008284;positive regulation of cell proliferation;0.0474795406709817;14172!GO:0001501;skeletal development;0.0474795406709817;14172!GO:0048646;anatomical structure formation;0.0474795406709817;14172!GO:0035295;tube development;0.0474795406709817;14172!GO:0001568;blood vessel development;0.0474795406709817;14172!GO:0001944;vasculature development;0.0474795406709817;14172!GO:0005125;cytokine 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|gostat_on_MCL_coexpression=GO:0001957;intramembranous ossification;0.00753218282791926;14172!GO:0002063;chondrocyte development;0.00753218282791926;14172!GO:0030949;positive regulation of vascular endothelial growth factor receptor signaling pathway;0.00753218282791926;14172!GO:0030947;regulation of vascular endothelial growth factor receptor signaling pathway;0.00753218282791926;14172!GO:0001958;endochondral ossification;0.00964040159283091;14172!GO:0048010;vascular endothelial growth factor receptor signaling pathway;0.0129087757991752;14172!GO:0002062;chondrocyte differentiation;0.0129087757991752;14172!GO:0005104;fibroblast growth factor receptor binding;0.014305658165835;14172!GO:0051216;cartilage development;0.0320994530025149;14172!GO:0030324;lung development;0.0325858050159078;14172!GO:0009967;positive regulation of signal transduction;0.0325858050159078;14172!GO:0030323;respiratory tube development;0.0325858050159078;14172!GO:0001503;ossification;0.0403599296141723;14172!GO:0031214;biomineral formation;0.0403599296141723;14172!GO:0046849;bone remodeling;0.0412656971515578;14172!GO:0048771;tissue remodeling;0.0454248818374421;14172!GO:0001525;angiogenesis;0.0474795406709817;14172!GO:0008083;growth factor activity;0.0474795406709817;14172!GO:0007169;transmembrane receptor protein tyrosine kinase signaling pathway;0.0474795406709817;14172!GO:0048514;blood vessel morphogenesis;0.0474795406709817;14172!GO:0008284;positive regulation of cell proliferation;0.0474795406709817;14172!GO:0001501;skeletal development;0.0474795406709817;14172!GO:0048646;anatomical structure formation;0.0474795406709817;14172!GO:0035295;tube development;0.0474795406709817;14172!GO:0001568;blood vessel development;0.0474795406709817;14172!GO:0001944;vasculature development;0.0474795406709817;14172!GO:0005125;cytokine activity;0.047486145639546;14172!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!1.30e-08!333;UBERON:0002048!1.45e-07!14;UBERON:0000117!1.45e-07!14;UBERON:0000171!1.45e-07!14;UBERON:0000170!1.45e-07!14;UBERON:0005597!1.45e-07!14;UBERON:0000118!1.45e-07!14
|tfbs_overrepresentation_for_novel_motifs=1.11639,0.369498,1.05921,0.480627,1.47084,0.495263,0.587291,0.206208,0.215218,0.219671,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,0.561256,1.75604,2.61348,0.586604,0.598814,0.29769,0.419327,0.62766,0.542568,0.516511,0.344372,2.03225,0.50223,0.897561,0.289148,0.964228,0.848378,1.10671,0.279977,0.57142,1.32199,0.230656,0.295233,2.18566,3.87129,0.317766,1.19315,1.18381,0.714592,1.31862,0.82704,0.347313,0.777641,0.654933,1.3744,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,1.80715,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.0869413,1.09164,0.17012,0.936963,2.92753,0.703064,0.859987,0.378988,0.212973,0.812889,1.59309,0.200155,0.975495,2.36627,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,2.47009,0.913319,0.71485,0.79664,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.990132,0.547992,1.27206,0.293461,0.0501572,1.21618,0.796633,0.757997,1.09707,0.745011,0.629509,1.67446,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,2.29762,3.0707,1.16374,0.620831,1.29374,0.275843,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.256263,1.04192,1.26486,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.227149
|tfbs_overrepresentation_jaspar=MA0003.1;1.08574,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;1.17655,MA0009.1;0.92425,MA0014.1;0.0200028,MA0017.1;0.89657,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;0.801219,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.362005,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.771749,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.0004304,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;0.0841779,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;1.0468,MA0103.1;0.348572,MA0105.1;0.488671,MA0106.1;0.677988,MA0107.1;2.45837,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;1.10833,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;0.113749,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;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;1.87278,MA0155.1;1.67164,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.127623,MA0163.1;0.519779,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.00878868,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:20, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:33047808..33047828,-p1@Fgf18
Mm9::chr2:110203061..110203070,-p7@Fibin
Mm9::chr2:110203142..110203158,-p2@Fibin
Mm9::chr2:110203249..110203259,-p5@Fibin
Mm9::chr2:110203272..110203287,-p4@Fibin
Mm9::chr2:110203292..110203308,-p3@Fibin
Mm9::chr2:110203314..110203338,-p1@Fibin


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:0001957intramembranous ossification0.00753218282791926
GO:0002063chondrocyte development0.00753218282791926
GO:0030949positive regulation of vascular endothelial growth factor receptor signaling pathway0.00753218282791926
GO:0030947regulation of vascular endothelial growth factor receptor signaling pathway0.00753218282791926
GO:0001958endochondral ossification0.00964040159283091
GO:0048010vascular endothelial growth factor receptor signaling pathway0.0129087757991752
GO:0002062chondrocyte differentiation0.0129087757991752
GO:0005104fibroblast growth factor receptor binding0.014305658165835
GO:0051216cartilage development0.0320994530025149
GO:0030324lung development0.0325858050159078
GO:0009967positive regulation of signal transduction0.0325858050159078
GO:0030323respiratory tube development0.0325858050159078
GO:0001503ossification0.0403599296141723
GO:0031214biomineral formation0.0403599296141723
GO:0046849bone remodeling0.0412656971515578
GO:0048771tissue remodeling0.0454248818374421
GO:0001525angiogenesis0.0474795406709817
GO:0008083growth factor activity0.0474795406709817
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0474795406709817
GO:0048514blood vessel morphogenesis0.0474795406709817
GO:0008284positive regulation of cell proliferation0.0474795406709817
GO:0001501skeletal development0.0474795406709817
GO:0048646anatomical structure formation0.0474795406709817
GO:0035295tube development0.0474795406709817
GO:0001568blood vessel development0.0474795406709817
GO:0001944vasculature development0.0474795406709817
GO:0005125cytokine activity0.047486145639546



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
multi-cellular organism1.30e-08333
lung1.45e-0714
respiratory tube1.45e-0714
respiration organ1.45e-0714
pair of lungs1.45e-0714
lung primordium1.45e-0714
lung bud1.45e-0714


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)
MA0003.11.08574
MA0004.10.481116
MA0006.10.311391
MA0007.11.17655
MA0009.10.92425
MA0014.10.0200028
MA0017.10.89657
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
MA0048.10.801219
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.771749
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0004304
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.10.488671
MA0106.10.677988
MA0107.12.45837
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
MA0139.11.10833
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
MA0039.20.113749
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.11.87278
MA0155.11.67164
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.127623
MA0163.10.519779
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.00878868
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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