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MCL coexpression mm9:1081: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003914!1.90e-09!47;UBERON:0007100!1.49e-07!18;UBERON:0000948!1.49e-07!18;UBERON:0005498!1.49e-07!18;UBERON:0004140!1.49e-07!18;UBERON:0009881!1.49e-07!18;UBERON:0004141!1.49e-07!18;UBERON:0003084!1.49e-07!18;UBERON:0007005!1.49e-07!18;UBERON:0004139!1.49e-07!18;UBERON:0004291!1.49e-07!18;UBERON:0004535!1.79e-07!23;UBERON:0001009!1.79e-07!23;UBERON:0000468!6.21e-07!333
|ontology_enrichment_uberon=UBERON:0003914!1.90e-09!47;UBERON:0007100!1.49e-07!18;UBERON:0000948!1.49e-07!18;UBERON:0005498!1.49e-07!18;UBERON:0004140!1.49e-07!18;UBERON:0009881!1.49e-07!18;UBERON:0004141!1.49e-07!18;UBERON:0003084!1.49e-07!18;UBERON:0007005!1.49e-07!18;UBERON:0004139!1.49e-07!18;UBERON:0004291!1.49e-07!18;UBERON:0004535!1.79e-07!23;UBERON:0001009!1.79e-07!23;UBERON:0000468!6.21e-07!333
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.660133,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.215218,0.0609112,1.34037,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.792229,0.19222,0.361892,0.374752,0.27937,1.45867,0.29769,0.419327,0.62766,0.184473,0.516511,2.46776,0.446946,0.50223,0.897561,0.289148,0.166577,0.316253,0.756613,0.766323,1.40099,1.32199,0.230656,0.295233,0.507468,0.54842,0.851774,0.822425,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,1.59614,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,1.02583,1.09164,0.17012,0.482617,0.166511,1.67636,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.146394,0.164297,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.127063,1.40122,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.982279,0.430942,1.02459,0.380122,0.547992,1.27206,0.796976,0.187586,0.484437,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,2.00769,0.595563,0.903645,1.19345,0.308038,1.00568,1.19218,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,1.81619,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.545091,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.227149
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.660133,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.215218,0.0609112,1.34037,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.792229,0.19222,0.361892,0.374752,0.27937,1.45867,0.29769,0.419327,0.62766,0.184473,0.516511,2.46776,0.446946,0.50223,0.897561,0.289148,0.166577,0.316253,0.756613,0.766323,1.40099,1.32199,0.230656,0.295233,0.507468,0.54842,0.851774,0.822425,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,1.59614,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,1.02583,1.09164,0.17012,0.482617,0.166511,1.67636,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.146394,0.164297,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.127063,1.40122,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.982279,0.430942,1.02459,0.380122,0.547992,1.27206,0.796976,0.187586,0.484437,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,2.00769,0.595563,0.903645,1.19345,0.308038,1.00568,1.19218,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,1.81619,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.545091,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.227149
|tfbs_overrepresentation_jaspar=MA0003.1;0.0286946,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.425579,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;2.04116,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;1.55156,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;0.0406078,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.656954,MA0061.1;0.724575,MA0063.1;0,MA0066.1;3.70678,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;0.0004304,MA0074.1;0.580087,MA0076.1;1.67548,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;1.07783,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;1.23749,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;0.488671,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;1.56464,MA0114.1;0.259463,MA0115.1;1.0246,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;0.600242,MA0139.1;1.10833,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.72625,MA0145.1;0.0910975,MA0146.1;0.264322,MA0147.1;0.274511,MA0148.1;1.24416,MA0149.1;0.411562,MA0062.2;2.93496,MA0035.2;0.573016,MA0039.2;0.367001,MA0138.2;0.727395,MA0002.2;0.592533,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;1.51738,MA0112.2;0.0910939,MA0065.2;0.0914071,MA0150.1;1.17631,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.336768,MA0156.1;2.52393,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.302441,MA0163.1;0.116706,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.432076,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}
}}

Revision as of 12:46, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:59653305..59653320,-p2@Cops3
Mm9::chr11:59653330..59653345,-p3@Cops3
Mm9::chr1:10028013..10028049,-p1@Cops5
Mm9::chr1:83311026..83311046,+p1@ENSMUST00000110799
p1@ENSMUST00000159051
Mm9::chr1:95375362..95375400,-p2@Hdlbp
Mm9::chr2:90894420..90894460,+p2@Psmc3
Mm9::chr4:118842570..118842574,-p@chr4:118842570..118842574
-


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:0008180signalosome0.00012312337623569
GO:0001701in utero embryonic development0.0119099506353932
GO:0043009chordate embryonic development0.02102104430441
GO:0009792embryonic development ending in birth or egg hatching0.02102104430441
GO:0005634nucleus0.036803317170155
GO:0043234protein complex0.036803317170155
GO:0009790embryonic development0.047157877500016



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
epithelial tube1.90e-0947
primary circulatory organ1.49e-0718
heart1.49e-0718
primitive heart tube1.49e-0718
primary heart field1.49e-0718
anterior lateral plate mesoderm1.49e-0718
heart tube1.49e-0718
heart primordium1.49e-0718
cardiac mesoderm1.49e-0718
cardiogenic plate1.49e-0718
heart rudiment1.49e-0718
cardiovascular system1.79e-0723
circulatory system1.79e-0723
multi-cellular organism6.21e-07333


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)
MA0003.10.0286946
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.425579
MA0017.10.337808
MA0019.10.740036
MA0024.12.04116
MA0025.11.15921
MA0027.12.57545
MA0028.11.55156
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
MA0055.10.0406078
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.656954
MA0061.10.724575
MA0063.10
MA0066.13.70678
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0004304
MA0074.10.580087
MA0076.11.67548
MA0077.10.905143
MA0078.10.670113
MA0081.11.07783
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.11.23749
MA0092.10.446857
MA0093.10.329976
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
MA0113.11.56464
MA0114.10.259463
MA0115.11.0246
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
MA0136.10.600242
MA0139.11.10833
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.72625
MA0145.10.0910975
MA0146.10.264322
MA0147.10.274511
MA0148.11.24416
MA0149.10.411562
MA0062.22.93496
MA0035.20.573016
MA0039.20.367001
MA0138.20.727395
MA0002.20.592533
MA0137.20.365364
MA0104.20.218974
MA0047.21.51738
MA0112.20.0910939
MA0065.20.0914071
MA0150.11.17631
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.336768
MA0156.12.52393
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.302441
MA0163.10.116706
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.432076
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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