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MCL coexpression mm9:751: Difference between revisions

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{{MCL_coexpression_mm9
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in the central nervous system;0.00827261272119652;18823!GO:0032291;ensheathment of axons in the central nervous system;0.00827261272119652;18823!GO:0050774;negative regulation of dendrite morphogenesis;0.00919078470315804;12704!GO:0022008;neurogenesis;0.00919078470315804;18823,12704!GO:0042759;long-chain fatty acid biosynthetic process;0.00919078470315804;18823!GO:0050773;regulation of dendrite development;0.00919078470315804;12704!GO:0048814;regulation of dendrite morphogenesis;0.00919078470315804;12704!GO:0014003;oligodendrocyte development;0.00919078470315804;18823!GO:0043209;myelin sheath;0.00919078470315804;18823!GO:0007091;mitotic metaphase/anaphase transition;0.0132336421865224;12704!GO:0048709;oligodendrocyte differentiation;0.0132942095545633;18823!GO:0021782;glial cell development;0.0132942095545633;18823!GO:0007399;nervous system development;0.0132942095545633;18823,12704!GO:0048813;dendrite morphogenesis;0.0153583731899625;12704!GO:0001676;long-chain fatty acid metabolic process;0.0154367110502175;18823!GO:0000070;mitotic sister chromatid segregation;0.0165379735355587;12704!GO:0000819;sister chromatid segregation;0.0165379735355587;12704!GO:0050768;negative regulation of neurogenesis;0.018374015336697;12704!GO:0000910;cytokinesis;0.0217557205028179;12704!GO:0042552;myelination;0.0217928865253435;18823!GO:0007272;ensheathment of neurons;0.0217928865253435;18823!GO:0008366;axon ensheathment;0.0217928865253435;18823!GO:0048468;cell development;0.0234178802114421;18823,12704!GO:0001726;ruffle;0.0234178802114421;12704!GO:0001508;regulation of action potential;0.0238737809030668;18823!GO:0010001;glial cell differentiation;0.0238737809030668;18823!GO:0016358;dendrite development;0.0238737809030668;12704!GO:0042063;gliogenesis;0.0242003900959857;18823!GO:0050767;regulation of neurogenesis;0.024520714674303;12704!GO:0019992;diacylglycerol binding;0.024520714674303;12704!GO:0007059;chromosome segregation;0.024520714674303;12704!GO:0006633;fatty acid biosynthetic process;0.0326644013582726;18823!GO:0046394;carboxylic acid biosynthetic process;0.0326644013582726;18823!GO:0016053;organic acid biosynthetic process;0.0326644013582726;18823!GO:0048731;system development;0.0326644013582726;18823,12704!GO:0048469;cell maturation;0.0326644013582726;18823!GO:0031252;leading edge;0.0326644013582726;12704!GO:0048869;cellular developmental process;0.0326644013582726;18823,12704!GO:0030154;cell differentiation;0.0326644013582726;18823,12704!GO:0021700;developmental maturation;0.0375475861361743;18823!GO:0048856;anatomical structure development;0.040054757706558;18823,12704!GO:0051093;negative regulation of developmental process;0.0408535308186507;12704!GO:0007275;multicellular organismal 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|gostat_on_MCL_coexpression=GO:0022010;myelination in the central nervous system;0.00827261272119652;18823!GO:0032291;ensheathment of axons in the central nervous system;0.00827261272119652;18823!GO:0050774;negative regulation of dendrite morphogenesis;0.00919078470315804;12704!GO:0022008;neurogenesis;0.00919078470315804;18823,12704!GO:0042759;long-chain fatty acid biosynthetic process;0.00919078470315804;18823!GO:0050773;regulation of dendrite development;0.00919078470315804;12704!GO:0048814;regulation of dendrite morphogenesis;0.00919078470315804;12704!GO:0014003;oligodendrocyte development;0.00919078470315804;18823!GO:0043209;myelin sheath;0.00919078470315804;18823!GO:0007091;mitotic metaphase/anaphase transition;0.0132336421865224;12704!GO:0048709;oligodendrocyte differentiation;0.0132942095545633;18823!GO:0021782;glial cell development;0.0132942095545633;18823!GO:0007399;nervous system development;0.0132942095545633;18823,12704!GO:0048813;dendrite morphogenesis;0.0153583731899625;12704!GO:0001676;long-chain fatty acid metabolic process;0.0154367110502175;18823!GO:0000070;mitotic sister chromatid segregation;0.0165379735355587;12704!GO:0000819;sister chromatid segregation;0.0165379735355587;12704!GO:0050768;negative regulation of neurogenesis;0.018374015336697;12704!GO:0000910;cytokinesis;0.0217557205028179;12704!GO:0042552;myelination;0.0217928865253435;18823!GO:0007272;ensheathment of neurons;0.0217928865253435;18823!GO:0008366;axon ensheathment;0.0217928865253435;18823!GO:0048468;cell development;0.0234178802114421;18823,12704!GO:0001726;ruffle;0.0234178802114421;12704!GO:0001508;regulation of action potential;0.0238737809030668;18823!GO:0010001;glial cell differentiation;0.0238737809030668;18823!GO:0016358;dendrite development;0.0238737809030668;12704!GO:0042063;gliogenesis;0.0242003900959857;18823!GO:0050767;regulation of neurogenesis;0.024520714674303;12704!GO:0019992;diacylglycerol binding;0.024520714674303;12704!GO:0007059;chromosome segregation;0.024520714674303;12704!GO:0006633;fatty acid biosynthetic process;0.0326644013582726;18823!GO:0046394;carboxylic acid biosynthetic process;0.0326644013582726;18823!GO:0016053;organic acid biosynthetic process;0.0326644013582726;18823!GO:0048731;system development;0.0326644013582726;18823,12704!GO:0048469;cell maturation;0.0326644013582726;18823!GO:0031252;leading edge;0.0326644013582726;12704!GO:0048869;cellular developmental process;0.0326644013582726;18823,12704!GO:0030154;cell differentiation;0.0326644013582726;18823,12704!GO:0021700;developmental maturation;0.0375475861361743;18823!GO:0048856;anatomical structure development;0.040054757706558;18823,12704!GO:0051093;negative regulation of developmental process;0.0408535308186507;12704!GO:0007275;multicellular organismal development;0.0478439283110007;18823,12704!
|ontology_enrichment_celltype=CL:0002610!1.49e-13!3;CL:0002614!3.45e-13!3;CL:0000117!5.37e-13!23;CL:0000337!5.37e-13!23;CL:0000540!1.26e-08!33;CL:0000047!1.26e-08!33;CL:0000031!1.26e-08!33;CL:0000404!1.26e-08!33;CL:0000393!4.41e-07!39;CL:0000211!4.41e-07!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.60e-23!54;UBERON:0001049!1.11e-18!52;UBERON:0005068!1.11e-18!52;UBERON:0006241!1.11e-18!52;UBERON:0007135!1.11e-18!52;UBERON:0001017!2.09e-18!73;UBERON:0001016!7.96e-18!75;UBERON:0002950!1.25e-16!4;UBERON:0001891!1.25e-16!4;UBERON:0009616!1.25e-16!4;UBERON:0010286!1.25e-16!4;UBERON:0002346!1.38e-16!64;UBERON:0003075!1.38e-16!64;UBERON:0007284!1.38e-16!64;UBERON:0004121!5.72e-15!95;UBERON:0000924!5.72e-15!95;UBERON:0006601!5.72e-15!95;UBERON:0003076!1.17e-14!12;UBERON:0003057!1.17e-14!12;UBERON:0010371!3.76e-14!73;UBERON:0004684!1.49e-13!3;UBERON:0002275!1.49e-13!3;UBERON:0002038!3.45e-13!3;UBERON:0009663!3.45e-13!3;UBERON:0009661!3.45e-13!3;UBERON:0000125!3.45e-13!3;UBERON:0002308!3.45e-13!3;UBERON:0002616!3.70e-12!46;UBERON:0000955!7.53e-12!47;UBERON:0006238!7.53e-12!47;UBERON:0010314!1.45e-10!92;UBERON:0002240!2.84e-10!6;UBERON:0005174!2.84e-10!6;UBERON:0001137!2.84e-10!6;UBERON:0002020!6.64e-10!34;UBERON:0001896!1.23e-08!2;UBERON:0002298!1.23e-08!2;UBERON:0005290!1.23e-08!2;UBERON:0010096!1.23e-08!2;UBERON:0003080!2.47e-08!40;UBERON:0003056!6.42e-08!49;UBERON:0001948!2.73e-07!5;UBERON:0002315!2.73e-07!5;UBERON:0002780!6.06e-07!39;UBERON:0001890!6.06e-07!39;UBERON:0006240!6.06e-07!39;UBERON:0000025!7.52e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,1.02163,0.645379,1.85288,0.495658,0.146465,0.154135,0.0330111,0.453212,0.484001,0.146657,0.507558,0.680035,0,0.696644,1.17871,1.34367,0.528436,0.296085,0.179861,0.50668,0.64218,0.895255,0.534339,1.30297,0.428336,0.739731,0.319094,0.414842,0.796599,0.218674,0.364174,0.242923,0.482999,0.210533,0.480503,0.559915,0.167387,0.637027,0.419787,0.371854,0.244285,0.0122159,0.383899,0.618203,0.443479,0.573356,0.271021,0.679429,0.560572,0.0915709,0.937018,0.954342,0.514504,1.39791,0.471658,0.12126,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.116281,1.17157,1.20707,0.607043,1.79385,0.299972,0.90463,0.713779,0.568383,0.436063,0.873141,0.0800961,0.0211263,0.0965007,0.623015,1.60001,1.15927,0.878077,1.89585,0.657661,0.188213,0.515495,0.444003,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.633313,0.10952,0.398075,0.697928,0.207304,0.993019,1.56109,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.041769,0.938577,0.178329,0.526881,1.01974,1.38016,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.442118
|tfbs_overrepresentation_jaspar=MA0003.1;0.00972621,MA0004.1;0.394951,MA0006.1;0.670874,MA0007.1;0.991467,MA0009.1;0.82278,MA0014.1;0.00813637,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.24786,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;1.73076,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.589612,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.424109,MA0056.1;0,MA0057.1;0.258928,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.169058,MA0061.1;0.194456,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.266547,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.00108891,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.0492918,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.109964,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;1.36684,MA0114.1;0.561811,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;1.20128,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.200183,MA0146.1;0.0548413,MA0147.1;0.593505,MA0148.1;1.86014,MA0149.1;4.29227,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.0156581,MA0138.2;0.630612,MA0002.2;0.447007,MA0137.2;0.287486,MA0104.2;0.476119,MA0047.2;2.27139,MA0112.2;0.0543294,MA0065.2;0.773848,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.0809407,MA0155.1;0.0631765,MA0156.1;0.763978,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0143037,MA0163.1;0.0600297,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.00996081,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.571417,MA0442.1;0
}}

Latest revision as of 15:49, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:10408741..10408754,-p@chr10:10408741..10408754
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Mm9::chr15:59373755..59373758,-p@chr15:59373755..59373758
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Mm9::chr3:32848711..32848733,-p@chr3:32848711..32848733
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Mm9::chr4:134073493..134073502,-p@chr4:134073493..134073502
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Mm9::chr4:134073503..134073512,-p@chr4:134073503..134073512
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Mm9::chr5:116456786..116456790,+p@chr5:116456786..116456790
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Mm9::chrX:133371161..133371170,+p@chrX:133371161..133371170
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Mm9::chrX:133371502..133371513,+p@chrX:133371502..133371513
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Mm9::chrX:133372506..133372513,+p@chrX:133372506..133372513
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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:0022010myelination in the central nervous system0.00827261272119652
GO:0032291ensheathment of axons in the central nervous system0.00827261272119652
GO:0050774negative regulation of dendrite morphogenesis0.00919078470315804
GO:0022008neurogenesis0.00919078470315804
GO:0042759long-chain fatty acid biosynthetic process0.00919078470315804
GO:0050773regulation of dendrite development0.00919078470315804
GO:0048814regulation of dendrite morphogenesis0.00919078470315804
GO:0014003oligodendrocyte development0.00919078470315804
GO:0043209myelin sheath0.00919078470315804
GO:0007091mitotic metaphase/anaphase transition0.0132336421865224
GO:0048709oligodendrocyte differentiation0.0132942095545633
GO:0021782glial cell development0.0132942095545633
GO:0007399nervous system development0.0132942095545633
GO:0048813dendrite morphogenesis0.0153583731899625
GO:0001676long-chain fatty acid metabolic process0.0154367110502175
GO:0000070mitotic sister chromatid segregation0.0165379735355587
GO:0000819sister chromatid segregation0.0165379735355587
GO:0050768negative regulation of neurogenesis0.018374015336697
GO:0000910cytokinesis0.0217557205028179
GO:0042552myelination0.0217928865253435
GO:0007272ensheathment of neurons0.0217928865253435
GO:0008366axon ensheathment0.0217928865253435
GO:0048468cell development0.0234178802114421
GO:0001726ruffle0.0234178802114421
GO:0001508regulation of action potential0.0238737809030668
GO:0010001glial cell differentiation0.0238737809030668
GO:0016358dendrite development0.0238737809030668
GO:0042063gliogenesis0.0242003900959857
GO:0050767regulation of neurogenesis0.024520714674303
GO:0019992diacylglycerol binding0.024520714674303
GO:0007059chromosome segregation0.024520714674303
GO:0006633fatty acid biosynthetic process0.0326644013582726
GO:0046394carboxylic acid biosynthetic process0.0326644013582726
GO:0016053organic acid biosynthetic process0.0326644013582726
GO:0048731system development0.0326644013582726
GO:0048469cell maturation0.0326644013582726
GO:0031252leading edge0.0326644013582726
GO:0048869cellular developmental process0.0326644013582726
GO:0030154cell differentiation0.0326644013582726
GO:0021700developmental maturation0.0375475861361743
GO:0048856anatomical structure development0.040054757706558
GO:0051093negative regulation of developmental process0.0408535308186507
GO:0007275multicellular organismal development0.0478439283110007



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
regional part of nervous system2.60e-2354
neural tube1.11e-1852
neural rod1.11e-1852
future spinal cord1.11e-1852
neural keel1.11e-1852
central nervous system2.09e-1873
nervous system7.96e-1875
regional part of midbrain1.25e-164
midbrain1.25e-164
presumptive midbrain1.25e-164
midbrain neural tube1.25e-164
neurectoderm1.38e-1664
neural plate1.38e-1664
presumptive neural plate1.38e-1664
ectoderm-derived structure5.72e-1595
ectoderm5.72e-1595
presumptive ectoderm5.72e-1595
posterior neural tube1.17e-1412
chordal neural plate1.17e-1412
ecto-epithelium3.76e-1473
raphe nuclei1.49e-133
reticular formation1.49e-133
substantia nigra3.45e-133
telencephalic nucleus3.45e-133
midbrain nucleus3.45e-133
neural nucleus3.45e-133
nucleus of brain3.45e-133
regional part of brain3.70e-1246
brain7.53e-1247
future brain7.53e-1247
structure with developmental contribution from neural crest1.45e-1092
spinal cord2.84e-106
dorsal region element2.84e-106
dorsum2.84e-106
gray matter6.64e-1034
medulla oblongata1.23e-082
brainstem1.23e-082
myelencephalon1.23e-082
future myelencephalon1.23e-082
anterior neural tube2.47e-0840
pre-chordal neural plate6.42e-0849
regional part of spinal cord2.73e-075
gray matter of spinal cord2.73e-075
regional part of forebrain6.06e-0739
forebrain6.06e-0739
future forebrain6.06e-0739
tube7.52e-07114


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)
MA0003.10.00972621
MA0004.10.394951
MA0006.10.670874
MA0007.10.991467
MA0009.10.82278
MA0014.10.00813637
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.11.73076
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.424109
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.266547
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.00108891
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.0492918
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
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
MA0113.11.36684
MA0114.10.561811
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.11.20128
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.200183
MA0146.10.0548413
MA0147.10.593505
MA0148.11.86014
MA0149.14.29227
MA0062.20.113962
MA0035.20.482026
MA0039.20.0156581
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.476119
MA0047.22.27139
MA0112.20.0543294
MA0065.20.773848
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.0631765
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0143037
MA0163.10.0600297
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.00996081
MA0102.21.5442
MA0258.10.180934
MA0259.10.571417
MA0442.10
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