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MCL coexpression mm9:1066: Difference between revisions

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{{MCL_coexpression_mm9
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regulation of interleukin-12 biosynthetic process;0.0169287240453624;18033!GO:0042090;interleukin-12 biosynthetic process;0.0338370468246374;18033!GO:0045075;regulation of interleukin-12 biosynthetic process;0.0338370468246374;18033!GO:0042036;negative regulation of cytokine biosynthetic process;0.0338370468246374;18033!GO:0016566;specific transcriptional repressor activity;0.0338370468246374;18033!GO:0032615;interleukin-12 production;0.0338370468246374;18033!GO:0048535;lymph node development;0.0410765854248425;18033!GO:0017148;negative regulation of translation;0.0488382460723203;18033!GO:0031327;negative regulation of cellular biosynthetic 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|gostat_on_MCL_coexpression=GO:0045083;negative regulation of interleukin-12 biosynthetic process;0.0169287240453624;18033!GO:0042090;interleukin-12 biosynthetic process;0.0338370468246374;18033!GO:0045075;regulation of interleukin-12 biosynthetic process;0.0338370468246374;18033!GO:0042036;negative regulation of cytokine biosynthetic process;0.0338370468246374;18033!GO:0016566;specific transcriptional repressor activity;0.0338370468246374;18033!GO:0032615;interleukin-12 production;0.0338370468246374;18033!GO:0048535;lymph node development;0.0410765854248425;18033!GO:0017148;negative regulation of translation;0.0488382460723203;18033!GO:0031327;negative regulation of cellular biosynthetic process;0.0488382460723203;18033!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.72e-18!48;UBERON:0002405!1.72e-18!48;UBERON:0002390!7.89e-17!45;UBERON:0003061!7.89e-17!45;UBERON:0000077!4.04e-12!35;UBERON:0004177!2.16e-11!29;UBERON:0005057!2.16e-11!29;UBERON:0003408!6.11e-10!24;UBERON:0002370!1.41e-09!23;UBERON:0000974!1.41e-09!23;UBERON:0004807!1.41e-09!23;UBERON:0005058!1.41e-09!23;UBERON:0003351!1.41e-09!23;UBERON:0009113!1.41e-09!23;UBERON:0003295!1.41e-09!23;UBERON:0009722!1.41e-09!23;UBERON:0005562!1.41e-09!23;UBERON:0007690!1.41e-09!23;UBERON:0001004!1.52e-09!42;UBERON:0003081!2.02e-09!87;UBERON:0000065!3.43e-09!41;UBERON:0006562!4.06e-09!24;UBERON:0001557!4.06e-09!24;UBERON:0001042!4.06e-09!24;UBERON:0008814!4.06e-09!24;UBERON:0009145!4.06e-09!24;UBERON:0000072!6.05e-08!27;UBERON:0004119!1.18e-07!118;UBERON:0000925!1.18e-07!118;UBERON:0006595!1.18e-07!118;UBERON:0001007!3.35e-07!116;UBERON:0001555!3.35e-07!116;UBERON:0007026!3.35e-07!116;UBERON:0001041!4.29e-07!80;UBERON:0000926!6.60e-07!120;UBERON:0004120!6.60e-07!120;UBERON:0006603!6.60e-07!120;UBERON:0002384!7.00e-07!46
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,1.20801,0.810002,0.495263,0.587291,0.206208,0.215218,0.0609112,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.112498,0.374752,0.988929,0.598814,0.80655,0.419327,0.62766,0.184473,0.516511,0.911169,0.446946,0.50223,0.897561,0.289148,0.498917,0.316253,0.248902,0.766323,0.57142,0.258564,0.230656,0.295233,0.507468,0.0742755,0.317766,0.277561,0.469348,0.714592,0.532496,0.0609361,0.347313,0.777641,0.654933,0.851157,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,1.02583,1.09164,0.507615,0.159969,0.166511,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,0.580284,0.975495,0.613286,0.042613,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.735764,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,1.13474,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.545091,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,1.42871
|tfbs_overrepresentation_jaspar=MA0003.1;1.4232,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;1.17655,MA0009.1;0.92425,MA0014.1;0.425579,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;0.157978,MA0056.1;0,MA0057.1;0.117936,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;2.05557,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.385183,MA0069.1;2.17466,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;1.56586,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;1.1347,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;2.16336,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;0.311187,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;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;3.11443,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.500692,MA0035.2;0.573016,MA0039.2;0.014361,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;0.126143,MA0155.1;0.102995,MA0156.1;1.67246,MA0157.1;1.83902,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.878466,MA0163.1;0.116706,MA0164.1;0.600609,MA0080.2;1.62792,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.065018,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::chr11:23662091..23662095,-p@chr11:23662091..23662095
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Mm9::chr12:60232412..60232456,+p2@Ctage5
Mm9::chr3:106592952..106592963,-p3@Cd53
Mm9::chr3:106592991..106593002,-p5@Cd53
Mm9::chr3:135354349..135354371,-p6@Nfkb1
Mm9::chr6:129182951..129182973,-p@chr6:129182951..129182973
-
Mm9::chr7:109398216..109398228,+p@chr7:109398216..109398228
+


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:0045083negative regulation of interleukin-12 biosynthetic process0.0169287240453624
GO:0042090interleukin-12 biosynthetic process0.0338370468246374
GO:0045075regulation of interleukin-12 biosynthetic process0.0338370468246374
GO:0042036negative regulation of cytokine biosynthetic process0.0338370468246374
GO:0016566specific transcriptional repressor activity0.0338370468246374
GO:0032615interleukin-12 production0.0338370468246374
GO:0048535lymph node development0.0410765854248425
GO:0017148negative regulation of translation0.0488382460723203
GO:0031327negative regulation of cellular biosynthetic process0.0488382460723203



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>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.72e-1848
immune system1.72e-1848
hematopoietic system7.89e-1745
blood island7.89e-1745
mixed endoderm/mesoderm-derived structure4.04e-1235
hemopoietic organ2.16e-1129
immune organ2.16e-1129
gland of gut6.11e-1024
thymus1.41e-0923
neck1.41e-0923
respiratory system epithelium1.41e-0923
hemolymphoid system gland1.41e-0923
pharyngeal epithelium1.41e-0923
thymic region1.41e-0923
pharyngeal gland1.41e-0923
entire pharyngeal arch endoderm1.41e-0923
thymus primordium1.41e-0923
early pharyngeal endoderm1.41e-0923
respiratory system1.52e-0942
lateral plate mesoderm2.02e-0987
respiratory tract3.43e-0941
pharynx4.06e-0924
upper respiratory tract4.06e-0924
chordate pharynx4.06e-0924
pharyngeal arch system4.06e-0924
pharyngeal region of foregut4.06e-0924
segment of respiratory tract6.05e-0827
endoderm-derived structure1.18e-07118
endoderm1.18e-07118
presumptive endoderm1.18e-07118
digestive system3.35e-07116
digestive tract3.35e-07116
primitive gut3.35e-07116
foregut4.29e-0780
mesoderm6.60e-07120
mesoderm-derived structure6.60e-07120
presumptive mesoderm6.60e-07120
connective tissue7.00e-0746


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)
MA0003.11.4232
MA0004.10.481116
MA0006.10.837454
MA0007.11.17655
MA0009.10.92425
MA0014.10.425579
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
MA0055.10.157978
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.12.05557
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.385183
MA0069.12.17466
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.11.56586
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
MA0090.11.1347
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.12.16336
MA0106.10.677988
MA0107.12.45837
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
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
MA0139.11.10833
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.72625
MA0145.10.0910975
MA0146.13.11443
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.500692
MA0035.20.573016
MA0039.20.014361
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
MA0154.10.126143
MA0155.10.102995
MA0156.11.67246
MA0157.11.83902
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.878466
MA0163.10.116706
MA0164.10.600609
MA0080.21.62792
MA0018.20.610433
MA0099.20.721008
MA0079.20.065018
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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