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MCL coexpression mm9:239: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0003939;L-iditol 2-dehydrogenase activity;0.0132825759081275;20322!GO:0003692;left-handed Z-DNA binding;0.0132825759081275;56417!GO:0005792;microsome;0.0132825759081275;56615,13105!GO:0042598;vesicular fraction;0.0132825759081275;56615,13105!GO:0016553;base conversion or substitution editing;0.0132825759081275;56417!GO:0003726;double-stranded RNA adenosine deaminase activity;0.0132825759081275;56417!GO:0003969;RNA editase activity;0.0151784233633089;56417!GO:0004000;adenosine deaminase activity;0.0265506003537321;56417!GO:0031047;RNA-mediated gene silencing;0.0320874135331278;56417!GO:0043169;cation binding;0.0320874135331278;20322,56417,213573,13105!GO:0006749;glutathione metabolic process;0.0320874135331278;56615!GO:0046872;metal ion binding;0.0320874135331278;20322,56417,213573,13105!GO:0009451;RNA modification;0.0320874135331278;56417!GO:0005624;membrane fraction;0.0320874135331278;56615,13105!GO:0043167;ion binding;0.0320874135331278;20322,56417,213573,13105!GO:0019239;deaminase activity;0.0320874135331278;56417!GO:0051287;NAD binding;0.0320874135331278;20322!GO:0004364;glutathione transferase activity;0.0320874135331278;56615!GO:0016814;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines;0.0320874135331278;56417!GO:0000267;cell fraction;0.0325170541772116;56615,13105!GO:0003725;double-stranded RNA binding;0.0325170541772116;56417!GO:0016458;gene silencing;0.0325170541772116;56417!GO:0050381;unspecific monooxygenase activity;0.0368429415700452;13105!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;0.0419004765711758;13105!GO:0005783;endoplasmic reticulum;0.0488021084113138;56615,13105!GO:0043566;structure-specific DNA binding;0.0488021084113138;56417!}}
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2-dehydrogenase activity;0.0132825759081275;20322!GO:0003692;left-handed Z-DNA binding;0.0132825759081275;56417!GO:0005792;microsome;0.0132825759081275;56615,13105!GO:0042598;vesicular fraction;0.0132825759081275;56615,13105!GO:0016553;base conversion or substitution editing;0.0132825759081275;56417!GO:0003726;double-stranded RNA adenosine deaminase activity;0.0132825759081275;56417!GO:0003969;RNA editase activity;0.0151784233633089;56417!GO:0004000;adenosine deaminase activity;0.0265506003537321;56417!GO:0031047;RNA-mediated gene silencing;0.0320874135331278;56417!GO:0043169;cation binding;0.0320874135331278;20322,56417,213573,13105!GO:0006749;glutathione metabolic process;0.0320874135331278;56615!GO:0046872;metal ion binding;0.0320874135331278;20322,56417,213573,13105!GO:0009451;RNA modification;0.0320874135331278;56417!GO:0005624;membrane fraction;0.0320874135331278;56615,13105!GO:0043167;ion binding;0.0320874135331278;20322,56417,213573,13105!GO:0019239;deaminase activity;0.0320874135331278;56417!GO:0051287;NAD binding;0.0320874135331278;20322!GO:0004364;glutathione transferase activity;0.0320874135331278;56615!GO:0016814;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines;0.0320874135331278;56417!GO:0000267;cell fraction;0.0325170541772116;56615,13105!GO:0003725;double-stranded RNA binding;0.0325170541772116;56417!GO:0016458;gene silencing;0.0325170541772116;56417!GO:0050381;unspecific monooxygenase activity;0.0368429415700452;13105!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;0.0419004765711758;13105!GO:0005783;endoplasmic reticulum;0.0488021084113138;56615,13105!GO:0043566;structure-specific DNA binding;0.0488021084113138;56417!|ontology_enrichment_celltype=CL:0000181!1.94e-30!5;CL:0000417!1.94e-30!5;CL:0000668!1.94e-30!5;CL:0000412!1.94e-30!5;CL:0000182!1.94e-30!5;CL:0000057!1.20e-07!1;CL:0000632!1.20e-07!1;CL:0000223!1.45e-07!20;CL:0000213!4.21e-07!1;CL:0002078!4.21e-07!1;CL:0000115!4.21e-07!1;CL:0002262!4.21e-07!1;CL:1000398!4.21e-07!1|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002107!5.27e-44!22;UBERON:0007499!5.27e-44!22;UBERON:0006925!5.27e-44!22;UBERON:0009497!5.27e-44!22;UBERON:0000015!5.27e-44!22;UBERON:0002423!5.27e-44!22;UBERON:0006235!5.27e-44!22;UBERON:0008835!5.27e-44!22;UBERON:0003894!5.27e-44!22;UBERON:0004161!5.27e-44!22;UBERON:0008836!5.27e-44!22;UBERON:0009854!4.90e-42!23;UBERON:0009856!4.90e-42!23;UBERON:0002365!1.44e-38!25;UBERON:0002330!1.44e-38!25;UBERON:0005256!8.22e-21!45;UBERON:0003914!7.29e-20!47;UBERON:0005172!5.41e-19!49;UBERON:0005173!5.41e-19!49;UBERON:0002417!5.41e-19!49;UBERON:0000916!5.41e-19!49;UBERON:0003929!9.30e-17!55;UBERON:0002368!3.10e-15!60;UBERON:0003104!5.84e-15!61;UBERON:0009142!5.84e-15!61;UBERON:0002530!6.06e-14!65;UBERON:0000490!1.04e-13!66;UBERON:0009569!1.04e-13!66;UBERON:0005911!4.81e-13!69;UBERON:0000949!1.96e-12!72;UBERON:0000466!3.43e-11!79;UBERON:0005177!3.43e-11!79;UBERON:0001041!4.96e-11!80;UBERON:0002100!1.27e-09!90;UBERON:0000025!3.08e-07!114;UBERON:0004921!3.08e-07!114;UBERON:0002394!4.21e-07!1;UBERON:0001281!4.21e-07!1;UBERON:0000353!4.21e-07!1;UBERON:0003497!4.21e-07!1;UBERON:0003909!4.21e-07!1;UBERON:0003928!4.21e-07!1;UBERON:0003835!4.21e-07!1;UBERON:0003513!4.21e-07!1;UBERON:0001280!4.21e-07!1;UBERON:0004647!4.21e-07!1;UBERON:0002294!4.21e-07!1;UBERON:0001173!4.21e-07!1;UBERON:0004912!4.21e-07!1;UBERON:0005171!4.21e-07!1;UBERON:0001007!4.40e-07!116;UBERON:0001555!4.40e-07!116;UBERON:0007026!4.40e-07!116;UBERON:0004119!6.21e-07!118;UBERON:0000925!6.21e-07!118;UBERON:0006595!6.21e-07!118|tfbs_overrepresentation_for_novel_motifs=0.179293,0.00927902,0.153339,1.77398,1.19201,0.518094,0.110102,0.271332,0.0231551,0.0115432,0.298295,0.339541,0.271958,0.116444,0.623969,0,0.234849,0.815106,0.0522006,0.0657439,1.22162,0.185087,0.115971,0.560033,0.0414548,0.131253,0.0463229,0.0771797,0.0219064,0.124738,0.07122,0.30824,0.058023,0.293878,0.0163808,0.0360958,0.0106492,0.102245,0.665404,0.0289707,0.833185,0.255568,0.351008,1.71745,0.000819181,0.0584129,0.182044,0.0841292,0.358785,0.456879,0.222867,0.146447,0.0530051,0.420411,0.434849,0.120215,1.1287,0.097776,0.328223,0.119133,0.293206,0.151943,1.06185,0.215255,0.126192,0.243043,0.551407,0.871196,0.289732,0.733632,0.03371,0.287041,8.53703e-05,1.17001,0.0015559,0.42545,0.45715,0.519366,0.767532,0.542079,0.157158,0.690461,1.44427,0.135299,0.368243,0.00014482,0.128218,0.0596859,0.544194,1.02598,0.613179,0.372211,0.852226,0.177821,0.00752625,0.093986,0.434111,0.857037,0.182205,0.419921,1.44182,1.50256,0.406109,0.635092,0.222555,0.0731931,0.264397,0.082328,0.0313268,0.0294324,0.389135,0.407566,0.86501,0.304852,0.619492,0.824889,8.09852e-05,0.0641298,0.235751,0.284166,0.467488,0.201353,0.13226,0.517993,0.668374,0.283227,0.366616,0.312808,0.550077,0.182027,0.392297,0.0598635,0.524295,0.40098,0.638919,0.0571551,0.0503022,0.0739723,1.45035,1.3849,0.995371,0.555542,0.430144,0.316186,0.218168,0.073569,0.541462,1.34592,0.744201,0.0137771,0.0237031,0.000412266,0.421705,0.00634974,0.399685,0.490348,0.14703,0.667257,0.704285,0.0502057,0.603336,0.367562,0.283555,0.384789,1.81337,1.27033,0.142447,1.13976,0.00264333|tfbs_overrepresentation_jaspar=MA0003.1;7.33034e-05,MA0004.1;0.062848,MA0006.1;0.0155229,MA0007.1;0.0571705,MA0009.1;0.875648,MA0014.1;0.00240805,MA0017.1;0.432206,MA0019.1;0.575474,MA0024.1;0.295217,MA0025.1;0.520387,MA0027.1;1.87879,MA0028.1;0.0173823,MA0029.1;0.27914,MA0030.1;0.283968,MA0031.1;0.716246,MA0038.1;0.410329,MA0040.1;0.338117,MA0041.1;0.961816,MA0042.1;0.316403,MA0043.1;0.405289,MA0046.1;0.356455,MA0048.1;0.0149481,MA0050.1;0.571422,MA0051.1;0.13618,MA0052.1;0.344399,MA0055.1;0.62832,MA0056.1;0,MA0057.1;0.238856,MA0058.1;0.0315409,MA0059.1;0.139654,MA0060.1;0.0888248,MA0061.1;0.252382,MA0063.1;0,MA0066.1;0.788488,MA0067.1;0.61835,MA0068.1;0.253074,MA0069.1;0.344664,MA0070.1;1.60605,MA0071.1;1.43874,MA0072.1;0.330543,MA0073.1;0.0441315,MA0074.1;0.106503,MA0076.1;0.0246789,MA0077.1;1.52373,MA0078.1;0.917137,MA0081.1;0.161577,MA0083.1;0.404641,MA0084.1;0.922325,MA0087.1;0.967552,MA0088.1;0.0299974,MA0089.1;0,MA0090.1;0.736993,MA0091.1;0.240385,MA0092.1;0.737946,MA0093.1;0.0848057,MA0095.1;0,MA0098.1;0,MA0100.1;0.330817,MA0101.1;0.147962,MA0103.1;0.243664,MA0105.1;0.0316657,MA0106.1;0.159832,MA0107.1;0.0214941,MA0108.2;1.79858,MA0109.1;0,MA0111.1;0.447568,MA0113.1;0.143312,MA0114.1;0.431582,MA0115.1;1.0502,MA0116.1;0.0154873,MA0117.1;0.381411,MA0119.1;0.619778,MA0122.1;0.397452,MA0124.1;0.571,MA0125.1;0.506387,MA0130.1;0,MA0131.1;0.195197,MA0132.1;0,MA0133.1;0,MA0135.1;0.435302,MA0136.1;0.116708,MA0139.1;0.00313416,MA0140.1;0.677264,MA0141.1;0.819189,MA0142.1;0.692442,MA0143.1;0.464815,MA0144.1;0.122105,MA0145.1;0.000983408,MA0146.1;0.00521216,MA0147.1;0.0099166,MA0148.1;2.44561,MA0149.1;0.153192,MA0062.2;0.0098309,MA0035.2;0.103023,MA0039.2;0.000283817,MA0138.2;0.19008,MA0002.2;0.143884,MA0137.2;0.112139,MA0104.2;0.00425077,MA0047.2;0.812951,MA0112.2;0.0150146,MA0065.2;0.229685,MA0150.1;0.795545,MA0151.1;0,MA0152.1;0.130846,MA0153.1;0.449181,MA0154.1;0.164285,MA0155.1;0.00716676,MA0156.1;0.0244806,MA0157.1;1.19766,MA0158.1;0,MA0159.1;0.302481,MA0160.1;0.52922,MA0161.1;0,MA0162.1;1.00435e-05,MA0163.1;0.0534736,MA0164.1;0.373396,MA0080.2;0.0946724,MA0018.2;0.77438,MA0099.2;1.04313,MA0079.2;0.0145073,MA0102.2;0.972341,MA0258.1;0.103447,MA0259.1;0.00860255,MA0442.1;0}}

Latest revision as of 14:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:124988598..124988600,+p@chr10:124988598..124988600
+
Mm9::chr10:36958849..36958852,+p@chr10:36958849..36958852
+
Mm9::chr10:94173889..94173890,-p@chr10:94173889..94173890
-
Mm9::chr11:118377098..118377101,+p@chr11:118377098..118377101
+
Mm9::chr15:82282802..82282815,+p1@Cyp2d9
Mm9::chr16:18410871..18410893,-p@chr16:18410871..18410893
-
Mm9::chr16:22899291..22899297,+p@chr16:22899291..22899297
+
Mm9::chr16:22899461..22899472,+p@chr16:22899461..22899472
+
Mm9::chr16:22899486..22899494,+p@chr16:22899486..22899494
+
Mm9::chr16:77838388..77838392,+p@chr16:77838388..77838392
+
Mm9::chr17:15914532..15914535,+p@chr17:15914532..15914535
+
Mm9::chr17:32067507..32067510,+p@chr17:32067507..32067510
+
Mm9::chr18:87925672..87925680,+p1@ENSMUST00000091776
Mm9::chr1:13864450..13864458,+p@chr1:13864450..13864458
+
Mm9::chr1:7167752..7167760,+p1@ENSMUST00000029124
Mm9::chr1:94791475..94791478,+p@chr1:94791475..94791478
+
Mm9::chr2:122060569..122060577,+p2@Sord
Mm9::chr2:156282978..156282979,+p@chr2:156282978..156282979
+
Mm9::chr2:172984701..172984706,+p@chr2:172984701..172984706
+
Mm9::chr3:14864162..14864173,+p@chr3:14864162..14864173
+
Mm9::chr3:89539611..89539638,+p@chr3:89539611..89539638
+
Mm9::chr4:50498164..50498166,+p@chr4:50498164..50498166
+
Mm9::chr4:60016350..60016358,+p1@Mup6
Mm9::chr4:61335128..61335131,-p1@LOC100048884
p1@Mup14
Mm9::chr4:61443256..61443260,-p2@Mup12
p2@Mup16
p2@Mup17
p2@Mup19
p2@Mup9
Mm9::chr4:61715146..61715151,-p1@Mup20
Mm9::chr5:127887029..127887031,+p@chr5:127887029..127887031
+
Mm9::chr5:44194868..44194871,+p@chr5:44194868..44194871
+
Mm9::chr6:138096234..138096265,+p@chr6:138096234..138096265
+
Mm9::chr6:138105225..138105237,+p@chr6:138105225..138105237
+
Mm9::chr7:112744083..112744109,-p@chr7:112744083..112744109
-
Mm9::chr7:148648620..148648622,+p12@Efcab4a
Mm9::chr8:13012412..13012413,+p@chr8:13012412..13012413
+
Mm9::chr9:120730227..120730233,+p@chr9:120730227..120730233
+
Mm9::chrX:45409736..45409738,+p@chrX:45409736..45409738
+


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:0003939L-iditol 2-dehydrogenase activity0.0132825759081275
GO:0003692left-handed Z-DNA binding0.0132825759081275
GO:0005792microsome0.0132825759081275
GO:0042598vesicular fraction0.0132825759081275
GO:0016553base conversion or substitution editing0.0132825759081275
GO:0003726double-stranded RNA adenosine deaminase activity0.0132825759081275
GO:0003969RNA editase activity0.0151784233633089
GO:0004000adenosine deaminase activity0.0265506003537321
GO:0031047RNA-mediated gene silencing0.0320874135331278
GO:0043169cation binding0.0320874135331278
GO:0006749glutathione metabolic process0.0320874135331278
GO:0046872metal ion binding0.0320874135331278
GO:0009451RNA modification0.0320874135331278
GO:0005624membrane fraction0.0320874135331278
GO:0043167ion binding0.0320874135331278
GO:0019239deaminase activity0.0320874135331278
GO:0051287NAD binding0.0320874135331278
GO:0004364glutathione transferase activity0.0320874135331278
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0320874135331278
GO:0000267cell fraction0.0325170541772116
GO:0003725double-stranded RNA binding0.0325170541772116
GO:0016458gene silencing0.0325170541772116
GO:0050381unspecific monooxygenase activity0.0368429415700452
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 oxygen0.0419004765711758
GO:0005783endoplasmic reticulum0.0488021084113138
GO:0043566structure-specific DNA binding0.0488021084113138



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
liver5.27e-4422
epithelial sac5.27e-4422
digestive gland5.27e-4422
epithelium of foregut-midgut junction5.27e-4422
anatomical boundary5.27e-4422
hepatobiliary system5.27e-4422
foregut-midgut junction5.27e-4422
hepatic diverticulum5.27e-4422
liver primordium5.27e-4422
septum transversum5.27e-4422
liver bud5.27e-4422
digestive tract diverticulum4.90e-4223
sac4.90e-4223
exocrine gland1.44e-3825
exocrine system1.44e-3825
trunk mesenchyme8.22e-2145
epithelial tube7.29e-2047
abdomen element5.41e-1949
abdominal segment element5.41e-1949
abdominal segment of trunk5.41e-1949
abdomen5.41e-1949
gut epithelium9.30e-1755
endocrine gland3.10e-1560
mesenchyme5.84e-1561
entire embryonic mesenchyme5.84e-1561
gland6.06e-1465
unilaminar epithelium1.04e-1366
subdivision of trunk1.04e-1366
endo-epithelium4.81e-1369
endocrine system1.96e-1272
immaterial anatomical entity3.43e-1179
trunk region element3.43e-1179
foregut4.96e-1180
trunk1.27e-0990
tube3.08e-07114
subdivision of digestive tract3.08e-07114
bile duct4.21e-071
hepatic sinusoid4.21e-071
parenchyma4.21e-071
abdomen blood vessel4.21e-071
sinusoid4.21e-071
digestive system duct4.21e-071
abdominal segment blood vessel4.21e-071
trunk blood vessel4.21e-071
liver parenchyma4.21e-071
liver lobule4.21e-071
biliary system4.21e-071
biliary tree4.21e-071
biliary bud4.21e-071
hepatic duct4.21e-071
digestive system4.40e-07116
digestive tract4.40e-07116
primitive gut4.40e-07116
endoderm-derived structure6.21e-07118
endoderm6.21e-07118
presumptive endoderm6.21e-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)
MA0003.17.33034e-05
MA0004.10.062848
MA0006.10.0155229
MA0007.10.0571705
MA0009.10.875648
MA0014.10.00240805
MA0017.10.432206
MA0019.10.575474
MA0024.10.295217
MA0025.10.520387
MA0027.11.87879
MA0028.10.0173823
MA0029.10.27914
MA0030.10.283968
MA0031.10.716246
MA0038.10.410329
MA0040.10.338117
MA0041.10.961816
MA0042.10.316403
MA0043.10.405289
MA0046.10.356455
MA0048.10.0149481
MA0050.10.571422
MA0051.10.13618
MA0052.10.344399
MA0055.10.62832
MA0056.10
MA0057.10.238856
MA0058.10.0315409
MA0059.10.139654
MA0060.10.0888248
MA0061.10.252382
MA0063.10
MA0066.10.788488
MA0067.10.61835
MA0068.10.253074
MA0069.10.344664
MA0070.11.60605
MA0071.11.43874
MA0072.10.330543
MA0073.10.0441315
MA0074.10.106503
MA0076.10.0246789
MA0077.11.52373
MA0078.10.917137
MA0081.10.161577
MA0083.10.404641
MA0084.10.922325
MA0087.10.967552
MA0088.10.0299974
MA0089.10
MA0090.10.736993
MA0091.10.240385
MA0092.10.737946
MA0093.10.0848057
MA0095.10
MA0098.10
MA0100.10.330817
MA0101.10.147962
MA0103.10.243664
MA0105.10.0316657
MA0106.10.159832
MA0107.10.0214941
MA0108.21.79858
MA0109.10
MA0111.10.447568
MA0113.10.143312
MA0114.10.431582
MA0115.11.0502
MA0116.10.0154873
MA0117.10.381411
MA0119.10.619778
MA0122.10.397452
MA0124.10.571
MA0125.10.506387
MA0130.10
MA0131.10.195197
MA0132.10
MA0133.10
MA0135.10.435302
MA0136.10.116708
MA0139.10.00313416
MA0140.10.677264
MA0141.10.819189
MA0142.10.692442
MA0143.10.464815
MA0144.10.122105
MA0145.10.000983408
MA0146.10.00521216
MA0147.10.0099166
MA0148.12.44561
MA0149.10.153192
MA0062.20.0098309
MA0035.20.103023
MA0039.20.000283817
MA0138.20.19008
MA0002.20.143884
MA0137.20.112139
MA0104.20.00425077
MA0047.20.812951
MA0112.20.0150146
MA0065.20.229685
MA0150.10.795545
MA0151.10
MA0152.10.130846
MA0153.10.449181
MA0154.10.164285
MA0155.10.00716676
MA0156.10.0244806
MA0157.11.19766
MA0158.10
MA0159.10.302481
MA0160.10.52922
MA0161.10
MA0162.11.00435e-05
MA0163.10.0534736
MA0164.10.373396
MA0080.20.0946724
MA0018.20.77438
MA0099.21.04313
MA0079.20.0145073
MA0102.20.972341
MA0258.10.103447
MA0259.10.00860255
MA0442.10
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