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MCL coexpression mm9:2801: Difference between revisions

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{{MCL_coexpression_mm9
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reticulum calcium ion homeostasis;0.0119794377064345;19164!GO:0042987;amyloid precursor protein catabolic process;0.0119794377064345;19164!GO:0051563;smooth endoplasmic reticulum calcium ion homeostasis;0.0119794377064345;19164!GO:0007220;Notch receptor processing;0.0134764982208395;19164!GO:0042982;amyloid precursor protein metabolic process;0.0143745376234029;19164!GO:0050435;beta-amyloid metabolic process;0.0163320167618723;19164!GO:0035253;ciliary rootlet;0.0163320167618723;19164!GO:0051605;protein maturation via proteolysis;0.0163320167618723;19164!GO:0042640;anagen;0.0163320167618723;19164!GO:0006516;glycoprotein catabolic process;0.0163320167618723;19164!GO:0051604;protein maturation;0.0163320167618723;19164!GO:0048820;hair follicle maturation;0.0193450377908991;19164!GO:0044441;cilium part;0.0193450377908991;19164!GO:0007613;memory;0.0218107238491664;19164!GO:0001708;cell fate specification;0.0275368557853909;19164!GO:0001756;somitogenesis;0.0329646854011658;19164!GO:0022404;molting cycle process;0.0329646854011658;19164!GO:0001942;hair follicle development;0.0329646854011658;19164!GO:0022405;hair cycle process;0.0329646854011658;19164!GO:0035282;segmentation;0.0329646854011658;19164!GO:0042633;hair cycle;0.0329646854011658;19164!GO:0042303;molting cycle;0.0329646854011658;19164!GO:0048589;developmental growth;0.0329646854011658;19164!GO:0030425;dendrite;0.0329646854011658;19164!GO:0007219;Notch signaling pathway;0.0329646854011658;19164!GO:0001764;neuron migration;0.0329646854011658;19164!GO:0043025;cell soma;0.0329646854011658;19164!GO:0006874;cellular calcium ion homeostasis;0.0329646854011658;19164!GO:0055074;calcium ion homeostasis;0.0329646854011658;19164!GO:0030424;axon;0.0329646854011658;19164!GO:0030326;embryonic limb morphogenesis;0.0329646854011658;19164!GO:0035113;embryonic appendage morphogenesis;0.0329646854011658;19164!GO:0006875;cellular metal ion homeostasis;0.0329646854011658;19164!GO:0005929;cilium;0.0329646854011658;19164!GO:0055065;metal ion homeostasis;0.0329646854011658;19164!GO:0007611;learning and/or memory;0.0329646854011658;19164!GO:0044463;cell projection part;0.0329646854011658;19164!GO:0035107;appendage morphogenesis;0.034550461439192;19164!GO:0035108;limb morphogenesis;0.034550461439192;19164!GO:0060173;limb development;0.034550461439192;19164!GO:0048736;appendage development;0.034550461439192;19164!GO:0045860;positive regulation of protein kinase activity;0.0348069740923052;19164!GO:0033674;positive regulation of kinase activity;0.0348069740923052;19164!GO:0051347;positive regulation of transferase activity;0.0348069740923052;19164!GO:0021700;developmental maturation;0.0348069740923052;19164!GO:0009952;anterior/posterior pattern formation;0.0348069740923052;19164!GO:0030005;cellular di-, tri-valent inorganic cation homeostasis;0.0348069740923052;19164!GO:0008544;epidermis development;0.0348069740923052;19164!GO:0055066;di-, tri-valent inorganic cation homeostasis;0.0348069740923052;19164!GO:0009100;glycoprotein metabolic process;0.0348069740923052;19164!GO:0045165;cell fate commitment;0.0348069740923052;19164!GO:0007398;ectoderm development;0.0348069740923052;19164!GO:0030003;cellular cation homeostasis;0.0351617043957099;19164!GO:0055080;cation homeostasis;0.0355031324513295;19164!GO:0043005;neuron projection;0.0377802262895967;19164!GO:0045859;regulation of protein kinase activity;0.0406119316614535;19164!GO:0043549;regulation of kinase activity;0.0409660595577061;19164!GO:0043085;positive regulation of catalytic activity;0.0409660595577061;19164!GO:0051338;regulation of transferase activity;0.0409660595577061;19164!GO:0055082;cellular chemical homeostasis;0.0424350545411579;19164!GO:0006873;cellular ion homeostasis;0.0424350545411579;19164!GO:0003002;regionalization;0.0424350545411579;19164!GO:0043065;positive regulation of 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|gostat_on_MCL_coexpression=GO:0032469;endoplasmic reticulum calcium ion homeostasis;0.0119794377064345;19164!GO:0042987;amyloid precursor protein catabolic process;0.0119794377064345;19164!GO:0051563;smooth endoplasmic reticulum calcium ion homeostasis;0.0119794377064345;19164!GO:0007220;Notch receptor processing;0.0134764982208395;19164!GO:0042982;amyloid precursor protein metabolic process;0.0143745376234029;19164!GO:0050435;beta-amyloid metabolic process;0.0163320167618723;19164!GO:0035253;ciliary rootlet;0.0163320167618723;19164!GO:0051605;protein maturation via proteolysis;0.0163320167618723;19164!GO:0042640;anagen;0.0163320167618723;19164!GO:0006516;glycoprotein catabolic process;0.0163320167618723;19164!GO:0051604;protein maturation;0.0163320167618723;19164!GO:0048820;hair follicle maturation;0.0193450377908991;19164!GO:0044441;cilium part;0.0193450377908991;19164!GO:0007613;memory;0.0218107238491664;19164!GO:0001708;cell fate specification;0.0275368557853909;19164!GO:0001756;somitogenesis;0.0329646854011658;19164!GO:0022404;molting cycle process;0.0329646854011658;19164!GO:0001942;hair follicle development;0.0329646854011658;19164!GO:0022405;hair cycle process;0.0329646854011658;19164!GO:0035282;segmentation;0.0329646854011658;19164!GO:0042633;hair cycle;0.0329646854011658;19164!GO:0042303;molting cycle;0.0329646854011658;19164!GO:0048589;developmental growth;0.0329646854011658;19164!GO:0030425;dendrite;0.0329646854011658;19164!GO:0007219;Notch signaling pathway;0.0329646854011658;19164!GO:0001764;neuron migration;0.0329646854011658;19164!GO:0043025;cell soma;0.0329646854011658;19164!GO:0006874;cellular calcium ion homeostasis;0.0329646854011658;19164!GO:0055074;calcium ion homeostasis;0.0329646854011658;19164!GO:0030424;axon;0.0329646854011658;19164!GO:0030326;embryonic limb morphogenesis;0.0329646854011658;19164!GO:0035113;embryonic appendage morphogenesis;0.0329646854011658;19164!GO:0006875;cellular metal ion homeostasis;0.0329646854011658;19164!GO:0005929;cilium;0.0329646854011658;19164!GO:0055065;metal ion homeostasis;0.0329646854011658;19164!GO:0007611;learning and/or memory;0.0329646854011658;19164!GO:0044463;cell projection part;0.0329646854011658;19164!GO:0035107;appendage morphogenesis;0.034550461439192;19164!GO:0035108;limb morphogenesis;0.034550461439192;19164!GO:0060173;limb development;0.034550461439192;19164!GO:0048736;appendage development;0.034550461439192;19164!GO:0045860;positive regulation of protein kinase activity;0.0348069740923052;19164!GO:0033674;positive regulation of kinase activity;0.0348069740923052;19164!GO:0051347;positive regulation of transferase activity;0.0348069740923052;19164!GO:0021700;developmental maturation;0.0348069740923052;19164!GO:0009952;anterior/posterior pattern formation;0.0348069740923052;19164!GO:0030005;cellular di-, tri-valent inorganic cation homeostasis;0.0348069740923052;19164!GO:0008544;epidermis development;0.0348069740923052;19164!GO:0055066;di-, tri-valent inorganic cation homeostasis;0.0348069740923052;19164!GO:0009100;glycoprotein metabolic process;0.0348069740923052;19164!GO:0045165;cell fate commitment;0.0348069740923052;19164!GO:0007398;ectoderm development;0.0348069740923052;19164!GO:0030003;cellular cation homeostasis;0.0351617043957099;19164!GO:0055080;cation homeostasis;0.0355031324513295;19164!GO:0043005;neuron projection;0.0377802262895967;19164!GO:0045859;regulation of protein kinase activity;0.0406119316614535;19164!GO:0043549;regulation of kinase activity;0.0409660595577061;19164!GO:0043085;positive regulation of catalytic activity;0.0409660595577061;19164!GO:0051338;regulation of transferase activity;0.0409660595577061;19164!GO:0055082;cellular chemical homeostasis;0.0424350545411579;19164!GO:0006873;cellular ion homeostasis;0.0424350545411579;19164!GO:0003002;regionalization;0.0424350545411579;19164!GO:0043065;positive regulation of apoptosis;0.0450445480303585;19164!GO:0043068;positive regulation of programmed cell death;0.0450445480303585;19164!GO:0050801;ion homeostasis;0.0450445480303585;19164!GO:0007166;cell surface receptor linked signal transduction;0.0450445480303585;19164,71862!GO:0007507;heart development;0.0453835450904017;19164!GO:0007420;brain development;0.0483799974998719;19164!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!5.76e-12!31;UBERON:0005409!4.30e-11!47;UBERON:0000344!3.05e-08!15;UBERON:0004923!9.58e-08!24;UBERON:0001242!3.20e-07!13;UBERON:0000060!3.20e-07!13;UBERON:0001262!3.20e-07!13;UBERON:0004786!3.20e-07!13
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.99159,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,1.38481,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.474221,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.777706,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,1.62246,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,1.94011,2.66432,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.421338
|tfbs_overrepresentation_jaspar=MA0003.1;0.526413,MA0004.1;1.8803,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.825079,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;1.49373,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.353763,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.557057,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.971751,MA0074.1;0.911576,MA0076.1;1.58243,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;1.51475,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;1.83298,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;1.44443,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;1.06145,MA0035.2;0.903829,MA0039.2;2.6396,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;1.21648,MA0047.2;0.962424,MA0112.2;0.794478,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;1.52001,MA0156.1;1.58027,MA0157.1;1.12772,MA0158.1;0,MA0159.1;1.39671,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.964824,MA0163.1;0.477233,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;1.4764,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;1.34197,MA0442.1;0
}}

Latest revision as of 19:06, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:85029073..85029199,+p1@Psen1
Mm9::chr2:163245244..163245284,-p1@3230401D17Rik
Mm9::chr3:30754868..30754924,+p1@Gpr160


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:0032469endoplasmic reticulum calcium ion homeostasis0.0119794377064345
GO:0042987amyloid precursor protein catabolic process0.0119794377064345
GO:0051563smooth endoplasmic reticulum calcium ion homeostasis0.0119794377064345
GO:0007220Notch receptor processing0.0134764982208395
GO:0042982amyloid precursor protein metabolic process0.0143745376234029
GO:0050435beta-amyloid metabolic process0.0163320167618723
GO:0035253ciliary rootlet0.0163320167618723
GO:0051605protein maturation via proteolysis0.0163320167618723
GO:0042640anagen0.0163320167618723
GO:0006516glycoprotein catabolic process0.0163320167618723
GO:0051604protein maturation0.0163320167618723
GO:0048820hair follicle maturation0.0193450377908991
GO:0044441cilium part0.0193450377908991
GO:0007613memory0.0218107238491664
GO:0001708cell fate specification0.0275368557853909
GO:0001756somitogenesis0.0329646854011658
GO:0022404molting cycle process0.0329646854011658
GO:0001942hair follicle development0.0329646854011658
GO:0022405hair cycle process0.0329646854011658
GO:0035282segmentation0.0329646854011658
GO:0042633hair cycle0.0329646854011658
GO:0042303molting cycle0.0329646854011658
GO:0048589developmental growth0.0329646854011658
GO:0030425dendrite0.0329646854011658
GO:0007219Notch signaling pathway0.0329646854011658
GO:0001764neuron migration0.0329646854011658
GO:0043025cell soma0.0329646854011658
GO:0006874cellular calcium ion homeostasis0.0329646854011658
GO:0055074calcium ion homeostasis0.0329646854011658
GO:0030424axon0.0329646854011658
GO:0030326embryonic limb morphogenesis0.0329646854011658
GO:0035113embryonic appendage morphogenesis0.0329646854011658
GO:0006875cellular metal ion homeostasis0.0329646854011658
GO:0005929cilium0.0329646854011658
GO:0055065metal ion homeostasis0.0329646854011658
GO:0007611learning and/or memory0.0329646854011658
GO:0044463cell projection part0.0329646854011658
GO:0035107appendage morphogenesis0.034550461439192
GO:0035108limb morphogenesis0.034550461439192
GO:0060173limb development0.034550461439192
GO:0048736appendage development0.034550461439192
GO:0045860positive regulation of protein kinase activity0.0348069740923052
GO:0033674positive regulation of kinase activity0.0348069740923052
GO:0051347positive regulation of transferase activity0.0348069740923052
GO:0021700developmental maturation0.0348069740923052
GO:0009952anterior/posterior pattern formation0.0348069740923052
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0348069740923052
GO:0008544epidermis development0.0348069740923052
GO:0055066di-, tri-valent inorganic cation homeostasis0.0348069740923052
GO:0009100glycoprotein metabolic process0.0348069740923052
GO:0045165cell fate commitment0.0348069740923052
GO:0007398ectoderm development0.0348069740923052
GO:0030003cellular cation homeostasis0.0351617043957099
GO:0055080cation homeostasis0.0355031324513295
GO:0043005neuron projection0.0377802262895967
GO:0045859regulation of protein kinase activity0.0406119316614535
GO:0043549regulation of kinase activity0.0409660595577061
GO:0043085positive regulation of catalytic activity0.0409660595577061
GO:0051338regulation of transferase activity0.0409660595577061
GO:0055082cellular chemical homeostasis0.0424350545411579
GO:0006873cellular ion homeostasis0.0424350545411579
GO:0003002regionalization0.0424350545411579
GO:0043065positive regulation of apoptosis0.0450445480303585
GO:0043068positive regulation of programmed cell death0.0450445480303585
GO:0050801ion homeostasis0.0450445480303585
GO:0007166cell surface receptor linked signal transduction0.0450445480303585
GO:0007507heart development0.0453835450904017
GO:0007420brain development0.0483799974998719



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
intestine5.76e-1231
gastrointestinal system4.30e-1147
mucosa3.05e-0815
organ component layer9.58e-0824
intestinal mucosa3.20e-0713
anatomical wall3.20e-0713
wall of intestine3.20e-0713
gastrointestinal system mucosa3.20e-0713


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)
MA0003.10.526413
MA0004.11.8803
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.11.49373
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.557057
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.971751
MA0074.10.911576
MA0076.11.58243
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.11.51475
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.11.83298
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.11.44443
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.21.06145
MA0035.20.903829
MA0039.22.6396
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.21.21648
MA0047.20.962424
MA0112.20.794478
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.11.52001
MA0156.11.58027
MA0157.11.12772
MA0158.10
MA0159.11.39671
MA0160.10.823568
MA0161.10
MA0162.10.964824
MA0163.10.477233
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.21.4764
MA0102.22.01714
MA0258.10.520639
MA0259.11.34197
MA0442.10
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