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MCL coexpression mm9:196: Difference between revisions

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{{MCL_coexpression_mm9
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monooxygenase activity;0.000381407618093475;13087,53973,13086!GO:0004497;monooxygenase activity;0.000381407618093475;14262,13087,53973,13086!GO:0016705;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;0.000381407618093475;14262,13087,53973,13086!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 oxygen;0.000381407618093475;13087,53973,13086!GO:0005792;microsome;0.000526622955370677;14262,13087,53973,13086!GO:0042598;vesicular fraction;0.000526622955370677;14262,13087,53973,13086!GO:0005624;membrane fraction;0.00162387099983086;14262,13087,53973,21816,13086!GO:0000267;cell fraction;0.00235617037791491;14262,13087,53973,21816,13086!GO:0020037;heme binding;0.00384637371565087;13087,53973,13086!GO:0046906;tetrapyrrole binding;0.00384637371565087;13087,53973,13086!GO:0006118;electron transport;0.00428262213647489;14262,13087,53973,13086!GO:0006091;generation of precursor metabolites and energy;0.0107482932718783;14262,13087,53973,13086!GO:0047685;amine sulfotransferase activity;0.0197017139437564;57430!GO:0032789;unsaturated monocarboxylic acid metabolic process;0.032001252598815;171281!GO:0032788;saturated monocarboxylic acid metabolic process;0.032001252598815;171281!GO:0015501;glutamate:sodium symporter activity;0.032001252598815;20511!GO:0005506;iron ion binding;0.0383846732732145;13087,53973,13086!GO:0050832;defense response to fungus;0.0383846732732145;66438!GO:0004813;alanine-tRNA ligase activity;0.0383846732732145;234734!GO:0006419;alanyl-tRNA aminoacylation;0.0383846732732145;234734!GO:0005783;endoplasmic reticulum;0.0399510662243412;14262,13087,53973,13086!GO:0015813;L-glutamate transport;0.0465064880593034;20511!GO:0016491;oxidoreductase activity;0.049463534248198;14262,13087,53973,13086!GO:0004499;flavin-containing monooxygenase activity;0.049463534248198;14262!GO:0015800;acidic amino acid transport;0.049463534248198;20511!GO:0005313;L-glutamate transmembrane transporter activity;0.049463534248198;20511!GO:0015172;acidic amino acid transmembrane transporter activity;0.049463534248198;20511!GO:0003810;protein-glutamine gamma-glutamyltransferase activity;0.049463534248198;21816!GO:0018149;peptide cross-linking;0.049463534248198;21816!GO:0005283;sodium:amino acid symporter activity;0.049463534248198;20511!GO:0000038;very-long-chain fatty acid metabolic 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.434704241352084,0.225301871178984,0.187437010020026,0.469723258307596,0.510563029767974,0.354876380541933,0,0,0,0,0,0,0,0,0,0,0.468513623788752,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.19106458117176,0,0,0,0,0,0,0,0,0.10536076625968,0,0.137398724818722,0.210606173730573,0.442174267268086,0.567139480176429,0.590469675984498,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0050381;unspecific monooxygenase activity;0.000381407618093475;13087,53973,13086!GO:0004497;monooxygenase activity;0.000381407618093475;14262,13087,53973,13086!GO:0016705;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;0.000381407618093475;14262,13087,53973,13086!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 oxygen;0.000381407618093475;13087,53973,13086!GO:0005792;microsome;0.000526622955370677;14262,13087,53973,13086!GO:0042598;vesicular fraction;0.000526622955370677;14262,13087,53973,13086!GO:0005624;membrane fraction;0.00162387099983086;14262,13087,53973,21816,13086!GO:0000267;cell fraction;0.00235617037791491;14262,13087,53973,21816,13086!GO:0020037;heme binding;0.00384637371565087;13087,53973,13086!GO:0046906;tetrapyrrole binding;0.00384637371565087;13087,53973,13086!GO:0006118;electron transport;0.00428262213647489;14262,13087,53973,13086!GO:0006091;generation of precursor metabolites and energy;0.0107482932718783;14262,13087,53973,13086!GO:0047685;amine sulfotransferase activity;0.0197017139437564;57430!GO:0032789;unsaturated monocarboxylic acid metabolic process;0.032001252598815;171281!GO:0032788;saturated monocarboxylic acid metabolic process;0.032001252598815;171281!GO:0015501;glutamate:sodium symporter activity;0.032001252598815;20511!GO:0005506;iron ion binding;0.0383846732732145;13087,53973,13086!GO:0050832;defense response to fungus;0.0383846732732145;66438!GO:0004813;alanine-tRNA ligase activity;0.0383846732732145;234734!GO:0006419;alanyl-tRNA aminoacylation;0.0383846732732145;234734!GO:0005783;endoplasmic reticulum;0.0399510662243412;14262,13087,53973,13086!GO:0015813;L-glutamate transport;0.0465064880593034;20511!GO:0016491;oxidoreductase activity;0.049463534248198;14262,13087,53973,13086!GO:0004499;flavin-containing monooxygenase activity;0.049463534248198;14262!GO:0015800;acidic amino acid transport;0.049463534248198;20511!GO:0005313;L-glutamate transmembrane transporter activity;0.049463534248198;20511!GO:0015172;acidic amino acid transmembrane transporter activity;0.049463534248198;20511!GO:0003810;protein-glutamine gamma-glutamyltransferase activity;0.049463534248198;21816!GO:0018149;peptide cross-linking;0.049463534248198;21816!GO:0005283;sodium:amino acid symporter activity;0.049463534248198;20511!GO:0000038;very-long-chain fatty acid metabolic process;0.049463534248198;171281!
|ontology_enrichment_celltype=CL:0000181!2.99e-19!5;CL:0000417!2.99e-19!5;CL:0000668!2.99e-19!5;CL:0000412!2.99e-19!5;CL:0000182!2.99e-19!5;CL:0000057!3.20e-07!1;CL:0000632!3.20e-07!1
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002107!2.14e-37!22;UBERON:0007499!2.14e-37!22;UBERON:0006925!2.14e-37!22;UBERON:0009497!2.14e-37!22;UBERON:0000015!2.14e-37!22;UBERON:0002423!2.14e-37!22;UBERON:0006235!2.14e-37!22;UBERON:0008835!2.14e-37!22;UBERON:0003894!2.14e-37!22;UBERON:0004161!2.14e-37!22;UBERON:0008836!2.14e-37!22;UBERON:0009854!1.02e-35!23;UBERON:0009856!1.02e-35!23;UBERON:0002365!9.27e-33!25;UBERON:0002330!9.27e-33!25;UBERON:0005256!1.32e-17!45;UBERON:0003914!8.53e-17!47;UBERON:0005172!4.72e-16!49;UBERON:0005173!4.72e-16!49;UBERON:0002417!4.72e-16!49;UBERON:0000916!4.72e-16!49;UBERON:0003929!3.83e-14!55;UBERON:0002368!7.65e-13!60;UBERON:0003104!1.31e-12!61;UBERON:0009142!1.31e-12!61;UBERON:0002530!9.69e-12!65;UBERON:0000490!1.54e-11!66;UBERON:0009569!1.54e-11!66;UBERON:0005911!5.68e-11!69;UBERON:0001041!5.79e-11!80;UBERON:0000949!1.88e-10!72;UBERON:0000466!2.18e-09!79;UBERON:0005177!2.18e-09!79;UBERON:0002100!4.76e-08!90;UBERON:0004921!3.42e-07!114;UBERON:0001007!4.88e-07!116;UBERON:0001555!4.88e-07!116;UBERON:0007026!4.88e-07!116;UBERON:0004119!6.88e-07!118;UBERON:0000925!6.88e-07!118;UBERON:0006595!6.88e-07!118
|tfbs_overrepresentation_for_novel_motifs=0.0832347,0.0435267,0.176324,0.273299,0.916211,0.864637,0.0570378,1.65118,0.105206,0.0122267,0.165198,0.434313,0.429319,0.0613893,0.16883,0,0.151552,0.620745,0.237092,0.233491,0.721548,0.105011,0.479131,1.20658,0.186079,0.251067,0.332789,0.142035,0.034761,0.287241,0.130144,0.610919,0.0558087,0.388814,0.00432198,0.0887713,0.00238167,0.192387,0.689543,0.0238196,0.893238,0.134446,0.27444,0.171962,0.127064,0.104749,0.354259,0.155947,0.577507,0.221488,0.141837,0.0827827,0.524883,0.311837,0.324872,0.0640069,0.237563,0.0487767,0.0549849,0.226514,0.200191,0.0868299,0.731651,0.135722,0.0682008,0.158253,1.10335,0.737254,1.08756,0.604513,0.153089,0.863025,0.00343537,0.350389,0.00657332,0.081002,0.0917007,0.104126,0.554558,0.481948,0.648552,0.486377,1.51496,0.0377021,0.265293,1.12372e-05,0.0142197,0.0602378,0.111994,0.888275,0.489957,0.2688,0.221396,0.950289,0.0349593,0.579932,0.594459,0.223247,0.10972,0.129709,0.37638,0.610488,0.809485,0.438141,0.436683,0.0331988,0.175924,0.351074,0.142789,0.134547,0.201441,0.300294,0.283011,0.385161,0.495912,0.630149,0.00584803,0.116055,0.152287,0.217361,0.933751,1.86041,1.37813,0.103696,0.542215,0.560088,0.0599118,0.216953,0.430801,0.0696842,0.781493,0.262018,0.40684,0.0691679,0.514273,8.3634,0.42624,0.135631,0.472714,1.2424,0.858301,1.1117,0.0773571,0.219861,0.138056,0.134826,2.36721,1.20376,0.431797,0.00340243,0.116725,9.60204e-05,0.313003,0.0746685,0.24256,0.979983,0.283084,0.0286432,0.401,0.0200032,0.480686,0.264692,0.560754,0.0169293,0.423227,0.867764,0.222848,0.19441,3.71198e-05
}}

Latest revision as of 14:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:33506521..33506543,-p@chr10:33506521..33506543
-
Mm9::chr10:33570806..33570810,+p@chr10:33570806..33570810
+
Mm9::chr10:33577516..33577519,+p1@Sult3a1
Mm9::chr10:79785781..79785791,-p10@Pcsk4
Mm9::chr12:73729820..73729827,-p@chr12:73729820..73729827
-
Mm9::chr12:80867845..80867864,+p@chr12:80867845..80867864
+
Mm9::chr12:80867869..80867911,+p@chr12:80867869..80867911
+
Mm9::chr12:85383465..85383477,+p@chr12:85383465..85383477
+
Mm9::chr12:85394299..85394333,+p@chr12:85394299..85394333
+
Mm9::chr13:35085097..35085115,-p7@Eci2
Mm9::chr14:56331943..56331947,-p2@Tgm1
Mm9::chr15:58876086..58876093,-p@chr15:58876086..58876093
-
Mm9::chr15:60752835..60752843,-p1@A1bg
Mm9::chr17:3463010..3463040,+p@chr17:3463010..3463040
+
Mm9::chr18:64639037..64639046,-p@chr18:64639037..64639046
-
Mm9::chr19:39961157..39961185,-p2@Cyp2c69
Mm9::chr19:39961220..39961250,-p1@Cyp2c69
Mm9::chr19:7876675..7876690,-p@chr19:7876675..7876690
-
Mm9::chr19:7877136..7877156,-p1@Slc22a26
Mm9::chr19:7877159..7877170,-p2@Slc22a26
Mm9::chr19:7877174..7877180,-p3@Slc22a26
Mm9::chr1:164914650..164914664,-p1@Fmo3
Mm9::chr1:191995926..191995933,+p@chr1:191995926..191995933
+
Mm9::chr1:36837940..36837957,+p@chr1:36837940..36837957
+
Mm9::chr1:89921716..89921733,+p1@ENSMUST00000119510
Mm9::chr1:90062579..90062612,+p1@Ugt1a5
Mm9::chr2:102546571..102546587,+p7@Slc1a2
Mm9::chr2:147872720..147872727,-p9@Foxa2
Mm9::chr2:34734962..34734966,+p@chr2:34734962..34734966
+
Mm9::chr2:5597037..5597071,-p4@Camk1d
Mm9::chr3:133454457..133454466,-p@chr3:133454457..133454466
-
Mm9::chr3:133454479..133454487,-p@chr3:133454479..133454487
-
Mm9::chr4:108811262..108811268,-p@chr4:108811262..108811268
-
Mm9::chr4:122648733..122648736,+p@chr4:122648733..122648736
+
Mm9::chr4:127199683..127199694,+p@chr4:127199683..127199694
+
Mm9::chr4:98697506..98697517,-p@chr4:98697506..98697517
-
Mm9::chr5:146345592..146345596,-p1@Cyp3a41a
p1@Cyp3a41b
Mm9::chr5:146531700..146531712,-p2@Cyp3a41a
p2@Cyp3a41b
Mm9::chr7:148237545..148237575,+p@chr7:148237545..148237575
+
Mm9::chr7:20278257..20278260,-p5@Apoc1
Mm9::chr7:26884144..26884148,+p@chr7:26884144..26884148
+
Mm9::chr7:27092210..27092216,+p1@Cyp2a4
Mm9::chr7:27620356..27620362,+p1@Cyp2a5
Mm9::chr7:31709188..31709204,-p1@Hamp2
Mm9::chr8:113560802..113560812,+p@chr8:113560802..113560812
+
Mm9::chr8:91106679..91106681,+p@chr8:91106679..91106681
+
Mm9::chr9:21639933..21639948,+p1@Gm6484
Mm9::chr9:21640079..21640090,+p@chr9:21640079..21640090
+
Mm9::chrX:20126832..20126843,+p2@Rgn


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:0050381unspecific monooxygenase activity0.000381407618093475
GO:0004497monooxygenase activity0.000381407618093475
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.000381407618093475
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 oxygen0.000381407618093475
GO:0005792microsome0.000526622955370677
GO:0042598vesicular fraction0.000526622955370677
GO:0005624membrane fraction0.00162387099983086
GO:0000267cell fraction0.00235617037791491
GO:0020037heme binding0.00384637371565087
GO:0046906tetrapyrrole binding0.00384637371565087
GO:0006118electron transport0.00428262213647489
GO:0006091generation of precursor metabolites and energy0.0107482932718783
GO:0047685amine sulfotransferase activity0.0197017139437564
GO:0032789unsaturated monocarboxylic acid metabolic process0.032001252598815
GO:0032788saturated monocarboxylic acid metabolic process0.032001252598815
GO:0015501glutamate:sodium symporter activity0.032001252598815
GO:0005506iron ion binding0.0383846732732145
GO:0050832defense response to fungus0.0383846732732145
GO:0004813alanine-tRNA ligase activity0.0383846732732145
GO:0006419alanyl-tRNA aminoacylation0.0383846732732145
GO:0005783endoplasmic reticulum0.0399510662243412
GO:0015813L-glutamate transport0.0465064880593034
GO:0016491oxidoreductase activity0.049463534248198
GO:0004499flavin-containing monooxygenase activity0.049463534248198
GO:0015800acidic amino acid transport0.049463534248198
GO:0005313L-glutamate transmembrane transporter activity0.049463534248198
GO:0015172acidic amino acid transmembrane transporter activity0.049463534248198
GO:0003810protein-glutamine gamma-glutamyltransferase activity0.049463534248198
GO:0018149peptide cross-linking0.049463534248198
GO:0005283sodium:amino acid symporter activity0.049463534248198
GO:0000038very-long-chain fatty acid metabolic process0.049463534248198



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 cell2.99e-195
endopolyploid cell2.99e-195
parenchymal cell2.99e-195
polyploid cell2.99e-195
hepatocyte2.99e-195
fibroblast3.20e-071
hepatic stellate cell3.20e-071

Uber Anatomy
Ontology termp-valuen
liver2.14e-3722
epithelial sac2.14e-3722
digestive gland2.14e-3722
epithelium of foregut-midgut junction2.14e-3722
anatomical boundary2.14e-3722
hepatobiliary system2.14e-3722
foregut-midgut junction2.14e-3722
hepatic diverticulum2.14e-3722
liver primordium2.14e-3722
septum transversum2.14e-3722
liver bud2.14e-3722
digestive tract diverticulum1.02e-3523
sac1.02e-3523
exocrine gland9.27e-3325
exocrine system9.27e-3325
trunk mesenchyme1.32e-1745
epithelial tube8.53e-1747
abdomen element4.72e-1649
abdominal segment element4.72e-1649
abdominal segment of trunk4.72e-1649
abdomen4.72e-1649
gut epithelium3.83e-1455
endocrine gland7.65e-1360
mesenchyme1.31e-1261
entire embryonic mesenchyme1.31e-1261
gland9.69e-1265
unilaminar epithelium1.54e-1166
subdivision of trunk1.54e-1166
endo-epithelium5.68e-1169
foregut5.79e-1180
endocrine system1.88e-1072
immaterial anatomical entity2.18e-0979
trunk region element2.18e-0979
trunk4.76e-0890
subdivision of digestive tract3.42e-07114
digestive system4.88e-07116
digestive tract4.88e-07116
primitive gut4.88e-07116
endoderm-derived structure6.88e-07118
endoderm6.88e-07118
presumptive endoderm6.88e-07118


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)
MA0003.15.96174e-10
MA0004.10.113515
MA0006.10.0723306
MA0007.10.1023
MA0009.10.651922
MA0014.11.82322e-06
MA0017.11.14607
MA0019.11.26449
MA0024.10.201902
MA0025.11.83562
MA0027.11.73381
MA0028.10.00469088
MA0029.11.05204
MA0030.11.68338
MA0031.10.509061
MA0038.10.0717608
MA0040.12.71402
MA0041.11.18319
MA0042.12.35786
MA0043.10.298253
MA0046.16.69001
MA0048.10.0172467
MA0050.10.955735
MA0051.10.553749
MA0052.10.244343
MA0055.10.0120324
MA0056.10
MA0057.10.00115216
MA0058.10.0526689
MA0059.10.536405
MA0060.10.0641488
MA0061.10.187126
MA0063.10
MA0066.10.238824
MA0067.10.494835
MA0068.10.114397
MA0069.10.244575
MA0070.10.669544
MA0071.10.144597
MA0072.10.232276
MA0073.14.52557e-06
MA0074.10.443625
MA0076.10.00759875
MA0077.11.16821
MA0078.11.04237
MA0081.10.366807
MA0083.10.297673
MA0084.10.786978
MA0087.10.266719
MA0088.10.0186664
MA0089.10
MA0090.10.426204
MA0091.10.294883
MA0092.11.4139
MA0093.10.0294259
MA0095.10
MA0098.10
MA0100.10.189403
MA0101.10.0639479
MA0103.10.395058
MA0105.10.000125033
MA0106.10.0927014
MA0107.10.21291
MA0108.20.827339
MA0109.10
MA0111.10.45991
MA0113.10.0804903
MA0114.11.23104
MA0115.10.812458
MA0116.10.481245
MA0117.10.276954
MA0119.10.852948
MA0122.10.291241
MA0124.10.450339
MA0125.10.390279
MA0130.10
MA0131.10.119827
MA0132.10
MA0133.10
MA0135.10.868613
MA0136.10.221605
MA0139.10.0869605
MA0140.10.421707
MA0141.10.260018
MA0142.10.488115
MA0143.10.614089
MA0144.10.188587
MA0145.10.210793
MA0146.13.11999e-05
MA0147.10.110424
MA0148.12.19794
MA0149.10.0670828
MA0062.20.000148268
MA0035.20.43048
MA0039.21.99301e-08
MA0138.20.115828
MA0002.20.279551
MA0137.20.442238
MA0104.20.0520505
MA0047.21.36722
MA0112.20.0485359
MA0065.20.140242
MA0150.10.47201
MA0151.10
MA0152.10.534196
MA0153.17.69984
MA0154.10.127142
MA0155.10.00233076
MA0156.10.0394812
MA0157.10.144034
MA0158.10
MA0159.10.831881
MA0160.10.304764
MA0161.10
MA0162.14.31864e-06
MA0163.10.00130726
MA0164.10.221989
MA0080.20.380707
MA0018.20.0652724
MA0099.20.112699
MA0079.21.68275e-14
MA0102.20.835781
MA0258.10.157368
MA0259.10.0400618
MA0442.10
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