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MCL coexpression mm9:486: Difference between revisions

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{{MCL_coexpression_mm9
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chain family amino acid biosynthetic process;0.0289243744861156;12035!GO:0050847;progesterone receptor signaling pathway;0.0289243744861156;18667!GO:0004084;branched-chain-amino-acid transaminase activity;0.0289243744861156;12035!GO:0002070;epithelial cell maturation;0.043176633121409;18667!GO:0009083;branched chain family amino acid catabolic process;0.043176633121409;12035!GO:0002064;epithelial cell development;0.043176633121409;18667!GO:0009081;branched chain family amino acid metabolic process;0.043176633121409;12035!GO:0001542;ovulation from ovarian follicle;0.043176633121409;18667!GO:0030728;ovulation;0.043176633121409;18667!GO:0030518;steroid hormone receptor signaling pathway;0.043176633121409;18667!GO:0030522;intracellular receptor-mediated signaling pathway;0.043176633121409;18667!GO:0030879;mammary gland development;0.043176633121409;18667!GO:0050678;regulation of epithelial cell proliferation;0.043176633121409;18667!GO:0008553;hydrogen-exporting ATPase activity, phosphorylative mechanism;0.043176633121409;11972!GO:0008483;transaminase activity;0.043176633121409;12035!GO:0022601;menstrual cycle phase;0.043176633121409;18667!GO:0022602;menstrual cycle process;0.043176633121409;18667!GO:0015985;energy coupled proton transport, down electrochemical gradient;0.043176633121409;11972!GO:0050673;epithelial cell proliferation;0.043176633121409;18667!GO:0015986;ATP synthesis coupled proton transport;0.043176633121409;11972!GO:0008652;amino acid biosynthetic process;0.043176633121409;12035!GO:0016769;transferase activity, transferring nitrogenous groups;0.043176633121409;12035!GO:0008585;female gonad development;0.043176633121409;18667!GO:0007292;female gamete generation;0.043176633121409;18667!GO:0006754;ATP biosynthetic process;0.043176633121409;11972!GO:0006753;nucleoside phosphate metabolic process;0.043176633121409;11972!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.043176633121409;11972!GO:0046545;development of primary female sexual characteristics;0.043176633121409;18667!GO:0030855;epithelial cell differentiation;0.043176633121409;18667!GO:0046660;female sex differentiation;0.043176633121409;18667!GO:0016469;proton-transporting two-sector ATPase complex;0.043176633121409;11972!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.043176633121409;11972!GO:0042698;menstrual cycle;0.043176633121409;18667!GO:0046034;ATP metabolic process;0.043176633121409;11972!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.043176633121409;11972!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.043176633121409;11972!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.043176633121409;11972!GO:0009063;amino acid catabolic process;0.043176633121409;12035!GO:0005496;steroid binding;0.043176633121409;18667!GO:0003707;steroid hormone receptor activity;0.043176633121409;18667!GO:0019829;cation-transporting ATPase activity;0.043176633121409;11972!GO:0004879;ligand-dependent nuclear receptor activity;0.043176633121409;18667!GO:0009142;nucleoside triphosphate biosynthetic process;0.043176633121409;11972!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.043176633121409;11972!GO:0009199;ribonucleoside triphosphate metabolic process;0.043176633121409;11972!GO:0006119;oxidative phosphorylation;0.043176633121409;11972!GO:0008406;gonad development;0.043176633121409;18667!GO:0009144;purine nucleoside triphosphate metabolic process;0.043176633121409;11972!GO:0015992;proton transport;0.043176633121409;11972!GO:0048608;reproductive structure development;0.043176633121409;18667!GO:0006752;group transfer coenzyme metabolic process;0.043176633121409;11972!GO:0044249;cellular biosynthetic process;0.043176633121409;11972,12035!GO:0009141;nucleoside triphosphate metabolic process;0.043176633121409;11972!GO:0044270;nitrogen compound catabolic process;0.043176633121409;12035!GO:0009310;amine 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|gostat_on_MCL_coexpression=GO:0009082;branched chain family amino acid biosynthetic process;0.0289243744861156;12035!GO:0050847;progesterone receptor signaling pathway;0.0289243744861156;18667!GO:0004084;branched-chain-amino-acid transaminase activity;0.0289243744861156;12035!GO:0002070;epithelial cell maturation;0.043176633121409;18667!GO:0009083;branched chain family amino acid catabolic process;0.043176633121409;12035!GO:0002064;epithelial cell development;0.043176633121409;18667!GO:0009081;branched chain family amino acid metabolic process;0.043176633121409;12035!GO:0001542;ovulation from ovarian follicle;0.043176633121409;18667!GO:0030728;ovulation;0.043176633121409;18667!GO:0030518;steroid hormone receptor signaling pathway;0.043176633121409;18667!GO:0030522;intracellular receptor-mediated signaling pathway;0.043176633121409;18667!GO:0030879;mammary gland development;0.043176633121409;18667!GO:0050678;regulation of epithelial cell proliferation;0.043176633121409;18667!GO:0008553;hydrogen-exporting ATPase activity, phosphorylative mechanism;0.043176633121409;11972!GO:0008483;transaminase activity;0.043176633121409;12035!GO:0022601;menstrual cycle phase;0.043176633121409;18667!GO:0022602;menstrual cycle process;0.043176633121409;18667!GO:0015985;energy coupled proton transport, down electrochemical gradient;0.043176633121409;11972!GO:0050673;epithelial cell proliferation;0.043176633121409;18667!GO:0015986;ATP synthesis coupled proton transport;0.043176633121409;11972!GO:0008652;amino acid biosynthetic process;0.043176633121409;12035!GO:0016769;transferase activity, transferring nitrogenous groups;0.043176633121409;12035!GO:0008585;female gonad development;0.043176633121409;18667!GO:0007292;female gamete generation;0.043176633121409;18667!GO:0006754;ATP biosynthetic process;0.043176633121409;11972!GO:0006753;nucleoside phosphate metabolic process;0.043176633121409;11972!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.043176633121409;11972!GO:0046545;development of primary female sexual characteristics;0.043176633121409;18667!GO:0030855;epithelial cell differentiation;0.043176633121409;18667!GO:0046660;female sex differentiation;0.043176633121409;18667!GO:0016469;proton-transporting two-sector ATPase complex;0.043176633121409;11972!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.043176633121409;11972!GO:0042698;menstrual cycle;0.043176633121409;18667!GO:0046034;ATP metabolic process;0.043176633121409;11972!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.043176633121409;11972!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.043176633121409;11972!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.043176633121409;11972!GO:0009063;amino acid catabolic process;0.043176633121409;12035!GO:0005496;steroid binding;0.043176633121409;18667!GO:0003707;steroid hormone receptor activity;0.043176633121409;18667!GO:0019829;cation-transporting ATPase activity;0.043176633121409;11972!GO:0004879;ligand-dependent nuclear receptor activity;0.043176633121409;18667!GO:0009142;nucleoside triphosphate biosynthetic process;0.043176633121409;11972!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.043176633121409;11972!GO:0009199;ribonucleoside triphosphate metabolic process;0.043176633121409;11972!GO:0006119;oxidative phosphorylation;0.043176633121409;11972!GO:0008406;gonad development;0.043176633121409;18667!GO:0009144;purine nucleoside triphosphate metabolic process;0.043176633121409;11972!GO:0015992;proton transport;0.043176633121409;11972!GO:0048608;reproductive structure development;0.043176633121409;18667!GO:0006752;group transfer coenzyme metabolic process;0.043176633121409;11972!GO:0044249;cellular biosynthetic process;0.043176633121409;11972,12035!GO:0009141;nucleoside triphosphate metabolic process;0.043176633121409;11972!GO:0044270;nitrogen compound catabolic process;0.043176633121409;12035!GO:0009310;amine catabolic process;0.043176633121409;12035!GO:0009152;purine ribonucleotide biosynthetic process;0.043176633121409;11972!GO:0006818;hydrogen transport;0.043176633121409;11972!GO:0045137;development of primary sexual characteristics;0.043176633121409;18667!GO:0009309;amine biosynthetic process;0.043176633121409;12035!GO:0015662;ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism;0.043176633121409;11972!GO:0009260;ribonucleotide biosynthetic process;0.043176633121409;11972!GO:0009150;purine ribonucleotide metabolic process;0.044532669425093;11972!GO:0006164;purine nucleotide biosynthetic process;0.044532669425093;11972!GO:0009259;ribonucleotide metabolic process;0.0449529148313214;11972!GO:0005923;tight junction;0.0449529148313214;21873!GO:0048609;reproductive process in a multicellular organism;0.0449529148313214;18667!GO:0032504;multicellular organism reproduction;0.0449529148313214;18667!GO:0007548;sex differentiation;0.0449529148313214;18667!GO:0048469;cell maturation;0.0449529148313214;18667!GO:0006163;purine nucleotide metabolic process;0.0449529148313214;11972!GO:0048732;gland development;0.0449529148313214;18667!GO:0044271;nitrogen compound biosynthetic process;0.0455191505253952;12035!GO:0042625;ATPase activity, coupled to transmembrane movement of ions;0.0478295860260173;11972!GO:0009108;coenzyme biosynthetic process;0.0483403062850561;11972!GO:0003006;reproductive developmental process;0.0494075198078521;18667!GO:0043296;apical junction complex;0.0496125512930327;21873!GO:0016327;apicolateral plasma membrane;0.0496125512930327;21873!GO:0015078;hydrogen ion transmembrane transporter activity;0.0496125512930327;11972!GO:0021700;developmental maturation;0.0496125512930327;18667!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000474!1.40e-47!9;UBERON:0003134!2.45e-42!8;UBERON:0003100!9.32e-39!11;UBERON:0003975!1.74e-27!5;UBERON:0005156!2.09e-23!26;UBERON:0000990!2.09e-23!26;UBERON:0005795!2.84e-22!4;UBERON:0000995!2.84e-22!4;UBERON:0004175!1.83e-21!9;UBERON:0003133!6.40e-21!24;UBERON:0005631!1.94e-16!3;UBERON:0000478!1.94e-16!3;UBERON:0000158!1.94e-16!3;UBERON:0000992!2.19e-16!3;UBERON:0001987!1.03e-11!2;UBERON:0003124!1.03e-11!2;UBERON:0004340!1.03e-11!2;UBERON:0001008!1.69e-09!19;UBERON:0004871!8.73e-08!3;UBERON:0004176!1.61e-07!17;UBERON:0009196!1.61e-07!17;UBERON:0009117!1.61e-07!17;UBERON:0000991!4.31e-07!18;UBERON:0005564!4.31e-07!18;UBERON:0006554!4.73e-07!18;UBERON:0006834!6.50e-07!1;UBERON:0000996!7.38e-07!1;UBERON:0000993!8.36e-07!1
|tfbs_overrepresentation_for_novel_motifs=0.595185,0.59339,0.186933,0.238864,0.356286,0.698129,1.56236,0.210111,0.223561,0.0916344,0.785008,0.314655,0.800979,0.335151,0.383709,0,0.505674,0.105493,0.0508204,0.409021,0.939233,0.138504,0.334384,0.353775,1.06882,0.35869,0.401215,0.736859,0.139679,0.867592,0.255771,0.598971,0.339783,0.15332,0.121176,3.97993,0.0985485,0.311629,0.290566,0.247011,0.349739,0.259911,1.30923,0.387037,0.147772,0.230148,0.433813,0.279902,0.564088,0.141659,0.48979,0.381972,0.11734,0.732469,0.749094,0.341233,0.147717,0.303999,0.166653,0.900327,0.580338,0.390204,0.0681609,0.479581,0.350748,0.516415,0.880067,1.22155,0.576002,1.07689,0.173229,0.0605055,0.150375,0.781142,0.040685,0.606791,0.98929,0.423705,0.564426,0.163487,0.479273,0.521544,1.00948,0.774743,0.671442,0.00202775,0.602992,0.297913,1.11664,1.38183,0.947651,0.676142,1.48408,0.365956,1.00206,0.0741053,1.20412,0.613539,0.43404,0.249401,0.667342,0.59871,0.715894,0.490329,2.12574,0.259558,0.543989,0.276621,0.16693,0.161774,0.201092,0.717588,0.493275,0.292444,0.954503,0.705468,0.0221978,0.678491,0.506861,0.096357,0.786314,0.46068,0.360259,1.08353,1.00724,0.567849,1.58681,0.60459,0.8786,0.115924,0.699779,0.233152,0.850049,0.352905,0.975524,0.135562,0.212784,0.261043,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,1.32835,0.436593,1.7082,0.214583,0.359158,0.0314055,0.00817433,0.733963,0.077277,1.65879,0.81211,0.382849,0.803531,0.590764,0.212571,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,0.323091,0.313326,0.0179486
}}

Latest revision as of 15:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:109005654..109005691,-p1@E030025P04Rik
Mm9::chr19:24200299..24200336,-p@chr19:24200299..24200336
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Mm9::chr19:60220585..60220600,+p1@ENSMUST00000065383
Mm9::chr3:79594253..79594277,-p@chr3:79594253..79594277
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Mm9::chr4:88526110..88526132,-p1@Ifne
Mm9::chr6:144996156..144996180,-p4@Bcat1
Mm9::chr6:82855186..82855200,-p@chr6:82855186..82855200
-
Mm9::chr8:108053276..108053315,-p@chr8:108053276..108053315
-
Mm9::chr9:53916368..53916376,-p4@Tnfaip8l3
Mm9::chr9:8899828..8899855,+p3@Pgr
Mm9::chr9:8900409..8900425,+p2@Pgr
Mm9::chr9:8900459..8900489,+p1@Pgr
Mm9::chr9:8900490..8900502,+p4@Pgr
Mm9::chr9:8900563..8900574,+p5@Pgr
Mm9::chr9:8901535..8901549,+p@chr9:8901535..8901549
+


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:0009082branched chain family amino acid biosynthetic process0.0289243744861156
GO:0050847progesterone receptor signaling pathway0.0289243744861156
GO:0004084branched-chain-amino-acid transaminase activity0.0289243744861156
GO:0002070epithelial cell maturation0.043176633121409
GO:0009083branched chain family amino acid catabolic process0.043176633121409
GO:0002064epithelial cell development0.043176633121409
GO:0009081branched chain family amino acid metabolic process0.043176633121409
GO:0001542ovulation from ovarian follicle0.043176633121409
GO:0030728ovulation0.043176633121409
GO:0030518steroid hormone receptor signaling pathway0.043176633121409
GO:0030522intracellular receptor-mediated signaling pathway0.043176633121409
GO:0030879mammary gland development0.043176633121409
GO:0050678regulation of epithelial cell proliferation0.043176633121409
GO:0008553hydrogen-exporting ATPase activity, phosphorylative mechanism0.043176633121409
GO:0008483transaminase activity0.043176633121409
GO:0022601menstrual cycle phase0.043176633121409
GO:0022602menstrual cycle process0.043176633121409
GO:0015985energy coupled proton transport, down electrochemical gradient0.043176633121409
GO:0050673epithelial cell proliferation0.043176633121409
GO:0015986ATP synthesis coupled proton transport0.043176633121409
GO:0008652amino acid biosynthetic process0.043176633121409
GO:0016769transferase activity, transferring nitrogenous groups0.043176633121409
GO:0008585female gonad development0.043176633121409
GO:0007292female gamete generation0.043176633121409
GO:0006754ATP biosynthetic process0.043176633121409
GO:0006753nucleoside phosphate metabolic process0.043176633121409
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.043176633121409
GO:0046545development of primary female sexual characteristics0.043176633121409
GO:0030855epithelial cell differentiation0.043176633121409
GO:0046660female sex differentiation0.043176633121409
GO:0016469proton-transporting two-sector ATPase complex0.043176633121409
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.043176633121409
GO:0042698menstrual cycle0.043176633121409
GO:0046034ATP metabolic process0.043176633121409
GO:0009145purine nucleoside triphosphate biosynthetic process0.043176633121409
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.043176633121409
GO:0009201ribonucleoside triphosphate biosynthetic process0.043176633121409
GO:0009063amino acid catabolic process0.043176633121409
GO:0005496steroid binding0.043176633121409
GO:0003707steroid hormone receptor activity0.043176633121409
GO:0019829cation-transporting ATPase activity0.043176633121409
GO:0004879ligand-dependent nuclear receptor activity0.043176633121409
GO:0009142nucleoside triphosphate biosynthetic process0.043176633121409
GO:0009205purine ribonucleoside triphosphate metabolic process0.043176633121409
GO:0009199ribonucleoside triphosphate metabolic process0.043176633121409
GO:0006119oxidative phosphorylation0.043176633121409
GO:0008406gonad development0.043176633121409
GO:0009144purine nucleoside triphosphate metabolic process0.043176633121409
GO:0015992proton transport0.043176633121409
GO:0048608reproductive structure development0.043176633121409
GO:0006752group transfer coenzyme metabolic process0.043176633121409
GO:0044249cellular biosynthetic process0.043176633121409
GO:0009141nucleoside triphosphate metabolic process0.043176633121409
GO:0044270nitrogen compound catabolic process0.043176633121409
GO:0009310amine catabolic process0.043176633121409
GO:0009152purine ribonucleotide biosynthetic process0.043176633121409
GO:0006818hydrogen transport0.043176633121409
GO:0045137development of primary sexual characteristics0.043176633121409
GO:0009309amine biosynthetic process0.043176633121409
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.043176633121409
GO:0009260ribonucleotide biosynthetic process0.043176633121409
GO:0009150purine ribonucleotide metabolic process0.044532669425093
GO:0006164purine nucleotide biosynthetic process0.044532669425093
GO:0009259ribonucleotide metabolic process0.0449529148313214
GO:0005923tight junction0.0449529148313214
GO:0048609reproductive process in a multicellular organism0.0449529148313214
GO:0032504multicellular organism reproduction0.0449529148313214
GO:0007548sex differentiation0.0449529148313214
GO:0048469cell maturation0.0449529148313214
GO:0006163purine nucleotide metabolic process0.0449529148313214
GO:0048732gland development0.0449529148313214
GO:0044271nitrogen compound biosynthetic process0.0455191505253952
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0478295860260173
GO:0009108coenzyme biosynthetic process0.0483403062850561
GO:0003006reproductive developmental process0.0494075198078521
GO:0043296apical junction complex0.0496125512930327
GO:0016327apicolateral plasma membrane0.0496125512930327
GO:0015078hydrogen ion transmembrane transporter activity0.0496125512930327
GO:0021700developmental maturation0.0496125512930327



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>


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)
MA0003.10.0773439
MA0004.10.239244
MA0006.10.37642
MA0007.10.227553
MA0009.10.623671
MA0014.10.0468601
MA0017.10.135289
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.10.12472
MA0029.10.562703
MA0030.10.568779
MA0031.11.32597
MA0038.10.942753
MA0040.10.635404
MA0041.10.536212
MA0042.10.172351
MA0043.10.71494
MA0046.10.657417
MA0048.10.102771
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.10.229093
MA0056.10
MA0057.10.703408
MA0058.10.968034
MA0059.11.00391
MA0060.10.071412
MA0061.10.0877629
MA0063.10
MA0066.12.49109
MA0067.10.953264
MA0068.10.0945752
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.11.14566
MA0074.10.318792
MA0076.10.148159
MA0077.10.605975
MA0078.11.80761
MA0081.11.07159
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.143884
MA0089.10
MA0090.10.212772
MA0091.10.24961
MA0092.11.79744
MA0093.10.40751
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.182791
MA0103.10.14251
MA0105.10.341877
MA0106.10.401864
MA0107.10.138378
MA0108.21.19989
MA0109.10
MA0111.11.1901
MA0113.10.983782
MA0114.10.291992
MA0115.10.717599
MA0116.10.37608
MA0117.10.686999
MA0119.10.183219
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.10.452196
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.891604
MA0139.11.67613
MA0140.10.30902
MA0141.10.155997
MA0142.10.522654
MA0143.10.391481
MA0144.10.617592
MA0145.10.541572
MA0146.10.00683492
MA0147.10.31605
MA0148.10.252062
MA0149.10.18682
MA0062.20.354916
MA0035.20.312946
MA0039.20.242567
MA0138.20.445088
MA0002.20.208749
MA0137.20.467774
MA0104.20.229221
MA0047.20.357963
MA0112.20.0124337
MA0065.22.42777
MA0150.11.20484
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.10.247047
MA0155.10.0157857
MA0156.10.45173
MA0157.11.23539
MA0158.10
MA0159.10.332142
MA0160.10.254455
MA0161.10
MA0162.10.0853381
MA0163.10.0738452
MA0164.10.335886
MA0080.20.848376
MA0018.20.344133
MA0099.20.439458
MA0079.21.24442
MA0102.21.32652
MA0258.10.0789466
MA0259.10.299239
MA0442.10
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