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MCL coexpression mm9:779: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0,0.0794416958658892,0.111406036636415,0,0,0.0672167371362732,0.132209189548857,0,0.0295481510864254,0.0373915887948828,0,0,0,0,0,0,0,0,0,0,0.019395466156359,0,0,0.125403512761718,0.121921047711406,0.0778523517070908,0.145836544144099,0.172522574498368,0,0,0.143098115334919,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00465955286320471,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0358287642816859,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0775747369966384,1.08298498874663,1.00866319882328,1.39646298488255,1.32131427413471,1.26838900684702,1.16828804859398,0.00759395162434266,0,0,0,0,0,0,0,0,0,1.22458500409906,0.0111115891581519,0.120145061331402,0.0143731259829272,0.0313116622716201,0.01830209728437,0.00677451755042,0.0391716470550344,0.0524779799464773,0.026771627933391,0.123242066792227,0,0,0.00962881004198613,0,0.0507733911376186,0,0,0.0109779846232158,0,0,0,0,0,0,0,0,0,0.00725514334883443,0,0.0333331749207566,0.0108727741554326,0,0,0,0,0.0135475403169392,0,0,0,0,0,0,0,0,0,0,0.00902987172550691,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0147026251165827,0.0289190162476046,0.117304124524544,0.126183949762189,0.15353244200018,0.167561021337489,0,0,0.0544210908033912,0,0,0,0,0,0,0.00840325517689797,0,0,0.0108192960527585,0,0,0.0309426291311886,0.0353563813294817,0.103843795198906,0,0,0,0,0,0.00633425810218652,0,0,0.014073973651282,0,1.67051963510541,0,0.00865934621344871,0.0195749335976853,0.0465309535923492,0.0588574860809232,0.114627313887731,0.235452588847387,0.233479726190846,0.359266798285661,0.25763631816348,0.171832510572742,0.16604909319849,0.55254007281166,0.589716419411467,0.658704187681587,0.0563840254372172,0,0,0,0,0,0.0103039948645527,0.00860183041341274,0.0351090996312627,0,0.0133572231937847,0.0497272303304926,0.0459263054347526,0.0370987661531283,0,0,0,0,0,0,0,0.0533303883224104,0.013232618438004,0,0,0,0,0,0,0,0,0,0.0171183089040912,0.0147001900089152,0.00728194448401683,0,0.0625417586327675,0,0,0,0,0.0258711457733664,0,0,0.0147132176406,0.0132520021813166,0.0347377536836739,0,0,0,0,0,0,0,0,0,0.0101723885111102,0.00927138242428978,0,0.0211178743798906,0.00722287919768502,0,0,0,0,0.00820824363229376,0,0,0,0,0,0,0,0,0,0.0646830188525658,0,0,0,0.00916200191272258,0.0270166926097271,0.0970119590937031,0.0508813388844863,0.0279670420235238,0,0,0,0,0,0,0,0,0.0107093437458465,0,0,0,0,0.0132510621324562,0,0,0,0,0,0.010395396787125,0.0124885411603974,0.0046415649776473,0.00354397049880978,0.0127522868457593,0.00448754016400604,0.0157113232769026,0.0101365005395677,0,0.00967402375073576,0,0,0.00852327301840361,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0191201314054533,0.016894628699881,0.00814381078431344,0.0727098821106063,0.0738343026855715,0.0459714366698242,0.0828522975247648,0.0306909430665103,0.0842044955332218,0.0658405278311428,0.0482593781936348,0.052981994730215,0.061619890519974,0.0473475840508051,0.0305460682084098,0.0166512351961611,0.0441794571613887,0.0963700552552707,0.051771451406792,0.0576923206666822,0.0708274169813171,0.0571667520514142,0.0426635435936905,0.0582926877426621,0.0280734562974354,0.0604956045702496,0.0363115123439563,0.0224737230636161,0.051452460206082,0.0165535779385604,0.0447446048891378,0.0220338961002423,0,0.0185206208503082,0.0683016639126177,0,0,0|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.789759981102069,0.808870401727249,1.23530355921389,1.03127295380734,1.03569349762126,1.22712073262545,0,0,0,0,0,0,0,0,0,0,1.14310160074284,0,0.0601091194109999,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.46922466685929,0,0,0,0,0,0,0,0,0,0,0,0,0,0.23491941546046,0.170978156452844,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|gostat_on_MCL_coexpression=GO:0048878;chemical homeostasis;0.000751951602892798;103988,84506,68938!GO:0042593;glucose homeostasis;0.000751951602892798;103988,68938!GO:0033500;carbohydrate homeostasis;0.000751951602892798;103988,68938!GO:0042592;homeostatic process;0.000907847436039409;103988,84506,68938!GO:0000267;cell fraction;0.00259532194131859;103988,13097,68938!GO:0051049;regulation of transport;0.00343572495553038;103988,68938!GO:0065008;regulation of biological quality;0.00343572495553038;103988,84506,68938!GO:0004340;glucokinase activity;0.00404195352970897;103988!GO:0032024;positive regulation of insulin secretion;0.00404195352970897;103988!GO:0005792;microsome;0.00658136694942709;13097,68938!GO:0042598;vesicular fraction;0.00658136694942709;13097,68938!GO:0050832;defense response to fungus;0.00909290069114756;84506!GO:0019725;cellular homeostasis;0.0100350514033023;103988,84506!GO:0001678;cell glucose homeostasis;0.0103893245423907;103988!GO:0043266;regulation of potassium ion transport;0.0103893245423907;103988!GO:0046323;glucose import;0.0103893245423907;68938!GO:0046324;regulation of glucose import;0.0103893245423907;68938!GO:0046835;carbohydrate phosphorylation;0.0103893245423907;103988!GO:0009898;internal side of plasma membrane;0.0103893245423907;68938!GO:0004396;hexokinase activity;0.0103893245423907;103988!GO:0000300;peripheral to membrane of membrane fraction;0.0103893245423907;68938!GO:0050796;regulation of insulin secretion;0.0181738477443164;103988!GO:0043269;regulation of ion transport;0.0189624563800178;103988!GO:0009620;response to fungus;0.0196850987954215;84506!GO:0006739;NADP metabolic process;0.0203496909631566;103988!GO:0005624;membrane fraction;0.0220875780328587;13097,68938!GO:0046883;regulation of hormone secretion;0.0269043085221581;103988!GO:0006769;nicotinamide metabolic process;0.0272316569735245;103988!GO:0030073;insulin secretion;0.0272316569735245;103988!GO:0019362;pyridine nucleotide metabolic process;0.0272316569735245;103988!GO:0055072;iron ion homeostasis;0.0272316569735245;84506!GO:0006879;cellular iron ion homeostasis;0.0272316569735245;84506!GO:0015758;glucose transport;0.0276980184414035;68938!GO:0008645;hexose transport;0.0276980184414035;68938!GO:0030072;peptide hormone secretion;0.0276980184414035;103988!GO:0015749;monosaccharide transport;0.0276980184414035;68938!GO:0002790;peptide secretion;0.0276980184414035;103988!GO:0019200;carbohydrate kinase activity;0.0276980184414035;103988!GO:0006733;oxidoreduction coenzyme metabolic process;0.0290280042862062;103988!GO:0050381;unspecific monooxygenase activity;0.0290280042862062;13097!GO:0048471;perinuclear region of cytoplasm;0.0309673661411862;68938!GO:0015833;peptide transport;0.0320500055687079;103988!GO:0016712;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of 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|ontology_enrichment_celltype=CL:0000181!3.82e-26!5;CL:0000417!3.82e-26!5;CL:0000668!3.82e-26!5;CL:0000412!3.82e-26!5;CL:0000182!3.82e-26!5;CL:0000057!3.65e-09!1;CL:0000632!3.65e-09!1;CL:0000223!8.99e-07!20
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002107!9.03e-23!22;UBERON:0007499!9.03e-23!22;UBERON:0006925!9.03e-23!22;UBERON:0009497!9.03e-23!22;UBERON:0000015!9.03e-23!22;UBERON:0002423!9.03e-23!22;UBERON:0006235!9.03e-23!22;UBERON:0008835!9.03e-23!22;UBERON:0003894!9.03e-23!22;UBERON:0004161!9.03e-23!22;UBERON:0008836!9.03e-23!22;UBERON:0009854!9.16e-22!23;UBERON:0009856!9.16e-22!23;UBERON:0002365!5.41e-20!25;UBERON:0002330!5.41e-20!25;UBERON:0005256!9.74e-14!45;UBERON:0005172!1.44e-12!49;UBERON:0005173!1.44e-12!49;UBERON:0002417!1.44e-12!49;UBERON:0000916!1.44e-12!49;UBERON:0003914!2.06e-10!47;UBERON:0002368!3.82e-10!60;UBERON:0003104!5.75e-10!61;UBERON:0009142!5.75e-10!61;UBERON:0002530!2.60e-09!65;UBERON:0009569!3.69e-09!66;UBERON:0003929!8.15e-09!55;UBERON:0000949!2.45e-08!72;UBERON:0005177!1.56e-07!79;UBERON:0000490!3.03e-07!66;UBERON:0005911!6.67e-07!69
|tfbs_overrepresentation_for_novel_motifs=0.93395,0.0206456,0.330161,0.394491,1.20555,0.40827,0.495658,0.448965,1.46248,0.133458,0.453212,0.484001,0.146657,0.507558,0.24249,0,0.696644,0.22065,0.419123,0.528436,1.45952,0.179861,0.50668,1.20034,0.337218,0.534339,1.30297,0.428336,0.268347,0.656973,0.414842,0.796599,0.218674,0.364174,0.242923,0.281474,0.210533,0.480503,0.191662,0.167387,0.637027,0.419787,0.663794,0.244285,0.059071,0.383899,0.618203,0.443479,0.904531,0.271021,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.279148,0.471658,0.12126,0.512521,0.776777,0.569793,0.952934,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.191038,2.2609,0.116281,0.107966,0.113315,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,0.14134,0.873141,0.0176817,0.092683,1.09342,0.623015,1.60001,1.15927,0.878077,0.809272,1.22553,0.188213,0.17334,0.444003,0.812053,0.618454,0.0816605,0.605162,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,1.18588,0.265919,0.398075,0.697928,0.597328,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,1.30862,1.18781,0.177062,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,1.70305,0.229209,0.32395,0.041769,0.938577,0.178329,0.526881,1.01974,1.38016,0.705025,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.12239
}}

Latest revision as of 15:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:120538639..120538669,+p11@Aspscr1
Mm9::chr11:5815129..5815144,-p1@Gck
Mm9::chr12:73729838..73729853,-p@chr12:73729838..73729853
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Mm9::chr12:73729855..73729874,-p@chr12:73729855..73729874
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Mm9::chr12:73729883..73729894,-p@chr12:73729883..73729894
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Mm9::chr12:73729916..73729925,-p@chr12:73729916..73729925
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Mm9::chr12:73729943..73729952,-p@chr12:73729943..73729952
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Mm9::chr19:39537557..39537571,-p1@Cyp2c38
Mm9::chr7:31729038..31729054,-p1@Hamp


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:0048878chemical homeostasis0.000751951602892798
GO:0042593glucose homeostasis0.000751951602892798
GO:0033500carbohydrate homeostasis0.000751951602892798
GO:0042592homeostatic process0.000907847436039409
GO:0000267cell fraction0.00259532194131859
GO:0051049regulation of transport0.00343572495553038
GO:0065008regulation of biological quality0.00343572495553038
GO:0004340glucokinase activity0.00404195352970897
GO:0032024positive regulation of insulin secretion0.00404195352970897
GO:0005792microsome0.00658136694942709
GO:0042598vesicular fraction0.00658136694942709
GO:0050832defense response to fungus0.00909290069114756
GO:0019725cellular homeostasis0.0100350514033023
GO:0001678cell glucose homeostasis0.0103893245423907
GO:0043266regulation of potassium ion transport0.0103893245423907
GO:0046323glucose import0.0103893245423907
GO:0046324regulation of glucose import0.0103893245423907
GO:0046835carbohydrate phosphorylation0.0103893245423907
GO:0009898internal side of plasma membrane0.0103893245423907
GO:0004396hexokinase activity0.0103893245423907
GO:0000300peripheral to membrane of membrane fraction0.0103893245423907
GO:0050796regulation of insulin secretion0.0181738477443164
GO:0043269regulation of ion transport0.0189624563800178
GO:0009620response to fungus0.0196850987954215
GO:0006739NADP metabolic process0.0203496909631566
GO:0005624membrane fraction0.0220875780328587
GO:0046883regulation of hormone secretion0.0269043085221581
GO:0006769nicotinamide metabolic process0.0272316569735245
GO:0030073insulin secretion0.0272316569735245
GO:0019362pyridine nucleotide metabolic process0.0272316569735245
GO:0055072iron ion homeostasis0.0272316569735245
GO:0006879cellular iron ion homeostasis0.0272316569735245
GO:0015758glucose transport0.0276980184414035
GO:0008645hexose transport0.0276980184414035
GO:0030072peptide hormone secretion0.0276980184414035
GO:0015749monosaccharide transport0.0276980184414035
GO:0002790peptide secretion0.0276980184414035
GO:0019200carbohydrate kinase activity0.0276980184414035
GO:0006733oxidoreduction coenzyme metabolic process0.0290280042862062
GO:0050381unspecific monooxygenase activity0.0290280042862062
GO:0048471perinuclear region of cytoplasm0.0309673661411862
GO:0015833peptide transport0.0320500055687079
GO:0016712oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen0.0320500055687079
GO:0006767water-soluble vitamin metabolic process0.0321432061621352
GO:0046879hormone secretion0.0330352193800603
GO:0006096glycolysis0.0354582835388274
GO:0051046regulation of secretion0.0382632967523427
GO:0006007glucose catabolic process0.0382632967523427
GO:0046365monosaccharide catabolic process0.0382632967523427
GO:0019320hexose catabolic process0.0382632967523427
GO:0005625soluble fraction0.0382632967523427
GO:0012506vesicle membrane0.0382632967523427
GO:0046164alcohol catabolic process0.0382632967523427
GO:0008643carbohydrate transport0.0408023295041978
GO:0006766vitamin metabolic process0.0408023295041978
GO:0044275cellular carbohydrate catabolic process0.0426450879325889
GO:0019898extrinsic to membrane0.0437905296077511
GO:0016052carbohydrate catabolic process0.0448955523849472
GO:0044444cytoplasmic part0.0462388432671752



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>

Cell Type
Ontology termp-valuen
metabolising cell3.82e-265
endopolyploid cell3.82e-265
parenchymal cell3.82e-265
polyploid cell3.82e-265
hepatocyte3.82e-265
fibroblast3.65e-091
hepatic stellate cell3.65e-091
endodermal cell8.99e-0720

Uber Anatomy
Ontology termp-valuen
liver9.03e-2322
epithelial sac9.03e-2322
digestive gland9.03e-2322
epithelium of foregut-midgut junction9.03e-2322
anatomical boundary9.03e-2322
hepatobiliary system9.03e-2322
foregut-midgut junction9.03e-2322
hepatic diverticulum9.03e-2322
liver primordium9.03e-2322
septum transversum9.03e-2322
liver bud9.03e-2322
digestive tract diverticulum9.16e-2223
sac9.16e-2223
exocrine gland5.41e-2025
exocrine system5.41e-2025
trunk mesenchyme9.74e-1445
abdomen element1.44e-1249
abdominal segment element1.44e-1249
abdominal segment of trunk1.44e-1249
abdomen1.44e-1249
epithelial tube2.06e-1047
endocrine gland3.82e-1060
mesenchyme5.75e-1061
entire embryonic mesenchyme5.75e-1061
gland2.60e-0965
subdivision of trunk3.69e-0966
gut epithelium8.15e-0955
endocrine system2.45e-0872
trunk region element1.56e-0779
unilaminar epithelium3.03e-0766
endo-epithelium6.67e-0769


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)
MA0003.10.00143485
MA0004.10.394951
MA0006.10.238555
MA0007.12.64186
MA0009.10.82278
MA0014.10.00813637
MA0017.10.726051
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.11.80346
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.14.24392
MA0042.13.19033
MA0043.10.918718
MA0046.10.858391
MA0048.10.281053
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.692644
MA0056.10
MA0057.10.0745664
MA0058.11.49242
MA0059.11.53319
MA0060.10.169058
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.0431817
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.413524
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.12.10074
MA0124.14.08836
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.77191
MA0146.10.0111657
MA0147.10.593505
MA0148.12.78137
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.20.0946163
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.476119
MA0047.20.533516
MA0112.20.200175
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.11.15501
MA0160.10.413266
MA0161.10
MA0162.10.0143037
MA0163.10.0124565
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.26.4867e-05
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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