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MCL coexpression mm9:313: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!3.79e-46!54;UBERON:0001016!2.62e-45!75;UBERON:0001017!5.81e-45!73;UBERON:0001049!2.31e-42!52;UBERON:0005068!2.31e-42!52;UBERON:0006241!2.31e-42!52;UBERON:0007135!2.31e-42!52;UBERON:0002346!1.02e-39!64;UBERON:0003075!1.02e-39!64;UBERON:0007284!1.02e-39!64;UBERON:0004121!1.62e-39!95;UBERON:0000924!1.62e-39!95;UBERON:0006601!1.62e-39!95;UBERON:0002020!2.33e-37!34;UBERON:0000955!1.54e-34!47;UBERON:0006238!1.54e-34!47;UBERON:0010371!2.20e-33!73;UBERON:0002616!3.34e-33!46;UBERON:0003528!1.50e-29!29;UBERON:0002791!1.50e-29!29;UBERON:0001893!1.50e-29!29;UBERON:0003056!1.43e-27!49;UBERON:0003080!1.77e-27!40;UBERON:0002780!3.77e-26!39;UBERON:0001890!3.77e-26!39;UBERON:0006240!3.77e-26!39;UBERON:0010314!4.29e-24!92;UBERON:0000956!5.32e-21!21;UBERON:0001869!5.32e-21!21;UBERON:0000203!5.32e-21!21;UBERON:0002619!9.77e-19!17;UBERON:0002021!1.06e-16!10;UBERON:0000411!1.06e-16!10;UBERON:0001950!1.06e-16!10;UBERON:0003076!3.72e-15!12;UBERON:0003057!3.72e-15!12;UBERON:0000025!1.98e-13!114;UBERON:0004111!7.31e-12!122;UBERON:0002240!2.52e-10!6;UBERON:0005174!2.52e-10!6;UBERON:0001137!2.52e-10!6;UBERON:0011216!8.00e-10!194;UBERON:0002420!1.60e-09!8;UBERON:0007245!1.60e-09!8;UBERON:0010009!1.60e-09!8;UBERON:0010011!1.60e-09!8;UBERON:0000454!1.60e-09!8;UBERON:0001948!5.80e-09!5;UBERON:0002315!5.80e-09!5;UBERON:0000064!9.55e-09!99;UBERON:0002950!4.66e-08!4;UBERON:0001891!4.66e-08!4;UBERON:0009616!4.66e-08!4;UBERON:0010286!4.66e-08!4;UBERON:0000483!1.89e-07!174;UBERON:0000477!1.97e-07!244;UBERON:0000119!3.04e-07!176;UBERON:0002038!9.60e-07!3;UBERON:0009663!9.60e-07!3;UBERON:0009661!9.60e-07!3;UBERON:0000125!9.60e-07!3;UBERON:0002308!9.60e-07!3
|ontology_enrichment_uberon=UBERON:0000073!3.79e-46!54;UBERON:0001016!2.62e-45!75;UBERON:0001017!5.81e-45!73;UBERON:0001049!2.31e-42!52;UBERON:0005068!2.31e-42!52;UBERON:0006241!2.31e-42!52;UBERON:0007135!2.31e-42!52;UBERON:0002346!1.02e-39!64;UBERON:0003075!1.02e-39!64;UBERON:0007284!1.02e-39!64;UBERON:0004121!1.62e-39!95;UBERON:0000924!1.62e-39!95;UBERON:0006601!1.62e-39!95;UBERON:0002020!2.33e-37!34;UBERON:0000955!1.54e-34!47;UBERON:0006238!1.54e-34!47;UBERON:0010371!2.20e-33!73;UBERON:0002616!3.34e-33!46;UBERON:0003528!1.50e-29!29;UBERON:0002791!1.50e-29!29;UBERON:0001893!1.50e-29!29;UBERON:0003056!1.43e-27!49;UBERON:0003080!1.77e-27!40;UBERON:0002780!3.77e-26!39;UBERON:0001890!3.77e-26!39;UBERON:0006240!3.77e-26!39;UBERON:0010314!4.29e-24!92;UBERON:0000956!5.32e-21!21;UBERON:0001869!5.32e-21!21;UBERON:0000203!5.32e-21!21;UBERON:0002619!9.77e-19!17;UBERON:0002021!1.06e-16!10;UBERON:0000411!1.06e-16!10;UBERON:0001950!1.06e-16!10;UBERON:0003076!3.72e-15!12;UBERON:0003057!3.72e-15!12;UBERON:0000025!1.98e-13!114;UBERON:0004111!7.31e-12!122;UBERON:0002240!2.52e-10!6;UBERON:0005174!2.52e-10!6;UBERON:0001137!2.52e-10!6;UBERON:0011216!8.00e-10!194;UBERON:0002420!1.60e-09!8;UBERON:0007245!1.60e-09!8;UBERON:0010009!1.60e-09!8;UBERON:0010011!1.60e-09!8;UBERON:0000454!1.60e-09!8;UBERON:0001948!5.80e-09!5;UBERON:0002315!5.80e-09!5;UBERON:0000064!9.55e-09!99;UBERON:0002950!4.66e-08!4;UBERON:0001891!4.66e-08!4;UBERON:0009616!4.66e-08!4;UBERON:0010286!4.66e-08!4;UBERON:0000483!1.89e-07!174;UBERON:0000477!1.97e-07!244;UBERON:0000119!3.04e-07!176;UBERON:0002038!9.60e-07!3;UBERON:0009663!9.60e-07!3;UBERON:0009661!9.60e-07!3;UBERON:0000125!9.60e-07!3;UBERON:0002308!9.60e-07!3
|tfbs_overrepresentation_for_novel_motifs=0.621914,0.939777,0.0766995,0.110767,0.319585,0.118683,0.515388,0.802044,0.850536,0.0595907,0.877815,0.165604,0.52939,0.181267,0.35264,0,0.321317,0.30426,0.473812,0.098583,0.825721,0.195815,0.180675,0.134743,0.274696,0.199623,0.980308,0.408692,0.184101,0.164643,0.122529,1.04073,0.126384,0.377102,0.039244,0.274443,0.028285,0.163319,0.0983182,0.194363,0.311778,0.125454,0.594452,0.356689,0.462897,0.341631,0.260475,0.432194,0.461946,0.735244,0.307679,0.218134,0.281475,0.524674,0.540069,0.185973,1.16882,0.476719,0.643173,0.184626,0.386651,0.224758,1.26811,0.298968,0.193388,0.330595,0.662968,0.992392,0.382806,0.851665,0.0683061,0.832259,0.00566097,0.569888,0.0357104,0.815322,0.376861,0.252107,0.973528,0.839858,0.33001,0.33504,0.223742,0.504682,0.468641,0.0202071,0.412576,0.302729,0.264106,1.14963,0.72731,0.472928,1.06401,0.942095,0.021752,0.972105,0.789568,0.416272,0.260664,0.397154,0.117729,0.403003,0.509378,0.308141,1.50003,0.394918,0.354606,0.137427,0.0645424,0.221421,0.289819,0.510939,0.489443,0.149001,0.733862,0.891587,0.0160363,0.362697,0.322341,1.18719,0.574718,0.773112,0.20086,0.700801,1.84473,0.375593,0.528274,0.408257,0.661578,0.955026,1.23783,0.106861,0.634573,0.195077,0.753996,0.190701,0.310556,0.793091,0.708276,1.51166,1.11861,0.667289,0.209097,0.411967,0.81698,0.396227,0.726958,1.47245,0.313761,0.0343953,0.076247,0.000436872,0.526055,0.414489,0.194455,0.598868,0.218838,0.165822,0.616083,0.641277,0.717087,0.467905,0.375957,0.28683,0.299755,0.1895,0.0279813,0.494051,0.153497
|tfbs_overrepresentation_for_novel_motifs=0.621914,0.939777,0.0766995,0.110767,0.319585,0.118683,0.515388,0.802044,0.850536,0.0595907,0.877815,0.165604,0.52939,0.181267,0.35264,0,0.321317,0.30426,0.473812,0.098583,0.825721,0.195815,0.180675,0.134743,0.274696,0.199623,0.980308,0.408692,0.184101,0.164643,0.122529,1.04073,0.126384,0.377102,0.039244,0.274443,0.028285,0.163319,0.0983182,0.194363,0.311778,0.125454,0.594452,0.356689,0.462897,0.341631,0.260475,0.432194,0.461946,0.735244,0.307679,0.218134,0.281475,0.524674,0.540069,0.185973,1.16882,0.476719,0.643173,0.184626,0.386651,0.224758,1.26811,0.298968,0.193388,0.330595,0.662968,0.992392,0.382806,0.851665,0.0683061,0.832259,0.00566097,0.569888,0.0357104,0.815322,0.376861,0.252107,0.973528,0.839858,0.33001,0.33504,0.223742,0.504682,0.468641,0.0202071,0.412576,0.302729,0.264106,1.14963,0.72731,0.472928,1.06401,0.942095,0.021752,0.972105,0.789568,0.416272,0.260664,0.397154,0.117729,0.403003,0.509378,0.308141,1.50003,0.394918,0.354606,0.137427,0.0645424,0.221421,0.289819,0.510939,0.489443,0.149001,0.733862,0.891587,0.0160363,0.362697,0.322341,1.18719,0.574718,0.773112,0.20086,0.700801,1.84473,0.375593,0.528274,0.408257,0.661578,0.955026,1.23783,0.106861,0.634573,0.195077,0.753996,0.190701,0.310556,0.793091,0.708276,1.51166,1.11861,0.667289,0.209097,0.411967,0.81698,0.396227,0.726958,1.47245,0.313761,0.0343953,0.076247,0.000436872,0.526055,0.414489,0.194455,0.598868,0.218838,0.165822,0.616083,0.641277,0.717087,0.467905,0.375957,0.28683,0.299755,0.1895,0.0279813,0.494051,0.153497
|tfbs_overrepresentation_jaspar=MA0003.1;0.0475636,MA0004.1;0.358028,MA0006.1;0.0376667,MA0007.1;0.336966,MA0009.1;0.425374,MA0014.1;0.000341065,MA0017.1;0.398085,MA0019.1;0.279241,MA0024.1;0.388875,MA0025.1;0.630472,MA0027.1;2.00714,MA0028.1;0.364782,MA0029.1;2.59587,MA0030.1;0.376415,MA0031.1;0.347586,MA0038.1;0.578883,MA0040.1;0.435948,MA0041.1;0.256066,MA0042.1;0.514842,MA0043.1;0.5085,MA0046.1;0.45588,MA0048.1;0.0168999,MA0050.1;0.414313,MA0051.1;0.593414,MA0052.1;0.442788,MA0055.1;0.0541681,MA0056.1;0,MA0057.1;0.108538,MA0058.1;0.231244,MA0059.1;0.246439,MA0060.1;0.0168335,MA0061.1;0.468254,MA0063.1;0,MA0066.1;1.06752,MA0067.1;0.732677,MA0068.1;0.796791,MA0069.1;0.443076,MA0070.1;0.434849,MA0071.1;0.81947,MA0072.1;0.427684,MA0073.1;0.0117568,MA0074.1;0.504232,MA0076.1;0.438642,MA0077.1;1.05438,MA0078.1;0.228674,MA0081.1;0.275922,MA0083.1;0.507806,MA0084.1;1.04444,MA0087.1;0.470385,MA0088.1;0.332218,MA0089.1;0,MA0090.1;0.64191,MA0091.1;0.376809,MA0092.1;0.310962,MA0093.1;0.381754,MA0095.1;0,MA0098.1;0,MA0100.1;0.161426,MA0101.1;0.257705,MA0103.1;0.188828,MA0105.1;0.361908,MA0106.1;0.66073,MA0107.1;0.181933,MA0108.2;0.296634,MA0109.1;0,MA0111.1;1.12049,MA0113.1;0.214338,MA0114.1;0.746323,MA0115.1;0.51095,MA0116.1;0.14839,MA0117.1;0.48285,MA0119.1;0.258451,MA0122.1;0.500096,MA0124.1;0.683426,MA0125.1;0.615761,MA0130.1;0,MA0131.1;0.27582,MA0132.1;0,MA0133.1;0,MA0135.1;3.37303,MA0136.1;0.181597,MA0139.1;0.302141,MA0140.1;0.486044,MA0141.1;1.223,MA0142.1;0.336004,MA0143.1;0.641011,MA0144.1;0.249943,MA0145.1;1.01256,MA0146.1;0.0438234,MA0147.1;0.11258,MA0148.1;0.381264,MA0149.1;0.0766295,MA0062.2;0.597388,MA0035.2;0.493344,MA0039.2;0.00121157,MA0138.2;0.743216,MA0002.2;0.153717,MA0137.2;0.457011,MA0104.2;0.175212,MA0047.2;0.199051,MA0112.2;0.763683,MA0065.2;1.01637,MA0150.1;0.10301,MA0151.1;0,MA0152.1;0.577815,MA0153.1;0.55531,MA0154.1;1.11864,MA0155.1;0.285814,MA0156.1;0.436777,MA0157.1;0.310784,MA0158.1;0,MA0159.1;0.29096,MA0160.1;0.385618,MA0161.1;0,MA0162.1;0.0318231,MA0163.1;0.342386,MA0164.1;0.181834,MA0080.2;0.0486268,MA0018.2;0.188226,MA0099.2;0.26517,MA0079.2;6.5347e-05,MA0102.2;1.09525,MA0258.1;0.691186,MA0259.1;0.252756,MA0442.1;0
}}
}}

Revision as of 11:32, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:87156375..87156383,-p@chr11:87156375..87156383
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Mm9::chr12:92812009..92812012,-p1@ENSMUST00000116715
Mm9::chr16:50420236..50420246,-p@chr16:50420236..50420246
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Mm9::chr17:37199615..37199652,+p9@Gabbr1
Mm9::chr17:57220111..57220144,+p@chr17:57220111..57220144
+
Mm9::chr17:57221069..57221081,-p@chr17:57221069..57221081
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Mm9::chr17:57221131..57221148,-p@chr17:57221131..57221148
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Mm9::chr18:31134922..31134933,-p@chr18:31134922..31134933
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Mm9::chr18:82754715..82754729,-p@chr18:82754715..82754729
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Mm9::chr19:8994922..8994936,+p3@B3gat3
Mm9::chr1:155756359..155756371,+p@chr1:155756359..155756371
+
Mm9::chr1:174204853..174204862,-p@chr1:174204853..174204862
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Mm9::chr1:174223797..174223808,-p@chr1:174223797..174223808
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Mm9::chr2:113632075..113632088,-p@chr2:113632075..113632088
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Mm9::chr2:170174741..170174743,-p@chr2:170174741..170174743
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Mm9::chr2:180889957..180889998,+p@chr2:180889957..180889998
+
Mm9::chr4:132999231..132999250,+p@chr4:132999231..132999250
+
Mm9::chr4:85034722..85034726,+p@chr4:85034722..85034726
+
Mm9::chr5:108948149..108948160,-p@chr5:108948149..108948160
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Mm9::chr5:139494354..139494365,-p@chr5:139494354..139494365
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Mm9::chr6:124711353..124711365,-p@chr6:124711353..124711365
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Mm9::chr6:124712740..124712754,-p@chr6:124712740..124712754
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Mm9::chr6:124716149..124716167,-p@chr6:124716149..124716167
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Mm9::chr7:152100513..152100528,-p@chr7:152100513..152100528
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Mm9::chr7:25784031..25784038,-p@chr7:25784031..25784038
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Mm9::chr8:73279849..73279867,+p4@Rab3a


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:0048790maintenance of presynaptic active zone structure0.00646469073576947
GO:0031630regulation of synaptic vesicle fusion to presynaptic membrane0.00646469073576947
GO:0051602response to electrical stimulus0.00646469073576947
GO:0031629synaptic vesicle fusion to presynaptic membrane0.00646469073576947
GO:0031338regulation of vesicle fusion0.00646469073576947
GO:0050975sensory perception of touch0.00646469073576947
GO:0006542glutamine biosynthetic process0.00861887926606475
GO:0004356glutamate-ammonia ligase activity0.00861887926606475
GO:0015018galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity0.00861887926606475
GO:0016211ammonia ligase activity0.0105768461489581
GO:0004965GABA-B receptor activity0.0105768461489581
GO:0006906vesicle fusion0.0119318713726987
GO:0016880acid-ammonia (or amide) ligase activity0.0119318713726987
GO:0016188synaptic vesicle maturation0.0129251316475187
GO:0003016respiratory system process0.0129251316475187
GO:0048488synaptic vesicle endocytosis0.0193829176417405
GO:0016079synaptic vesicle exocytosis0.0250775914657576
GO:0016050vesicle organization and biogenesis0.0251874396635394
GO:0007274neuromuscular synaptic transmission0.0251874396635394
GO:0009084glutamine family amino acid biosynthetic process0.0251874396635394
GO:0006541glutamine metabolic process0.0276739554004592
GO:0017157regulation of exocytosis0.0316914421788287
GO:0015020glucuronosyltransferase activity0.0319950096254669
GO:0006944membrane fusion0.0354944803059186
GO:0048489synaptic vesicle transport0.0356206229408446
GO:0008067metabotropic glutamate, GABA-B-like receptor activity0.0387085213234202
GO:0016917GABA receptor activity0.0401355710100174
GO:0009064glutamine family amino acid metabolic process0.0413610703076045
GO:0009791post-embryonic development0.0413610703076045
GO:0005737cytoplasm0.0423500080886129
GO:0008652amino acid biosynthetic process0.0436708464995313



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 system3.79e-4654
nervous system2.62e-4575
central nervous system5.81e-4573
neural tube2.31e-4252
neural rod2.31e-4252
future spinal cord2.31e-4252
neural keel2.31e-4252
neurectoderm1.02e-3964
neural plate1.02e-3964
presumptive neural plate1.02e-3964
ectoderm-derived structure1.62e-3995
ectoderm1.62e-3995
presumptive ectoderm1.62e-3995
gray matter2.33e-3734
brain1.54e-3447
future brain1.54e-3447
ecto-epithelium2.20e-3373
regional part of brain3.34e-3346
brain grey matter1.50e-2929
regional part of telencephalon1.50e-2929
telencephalon1.50e-2929
pre-chordal neural plate1.43e-2749
anterior neural tube1.77e-2740
regional part of forebrain3.77e-2639
forebrain3.77e-2639
future forebrain3.77e-2639
structure with developmental contribution from neural crest4.29e-2492
cerebral cortex5.32e-2121
cerebral hemisphere5.32e-2121
pallium5.32e-2121
regional part of cerebral cortex9.77e-1917
occipital lobe1.06e-1610
visual cortex1.06e-1610
neocortex1.06e-1610
posterior neural tube3.72e-1512
chordal neural plate3.72e-1512
tube1.98e-13114
anatomical conduit7.31e-12122
spinal cord2.52e-106
dorsal region element2.52e-106
dorsum2.52e-106
organ system subdivision8.00e-10194
basal ganglion1.60e-098
nuclear complex of neuraxis1.60e-098
aggregate regional part of brain1.60e-098
collection of basal ganglia1.60e-098
cerebral subcortex1.60e-098
regional part of spinal cord5.80e-095
gray matter of spinal cord5.80e-095
organ part9.55e-0999
regional part of midbrain4.66e-084
midbrain4.66e-084
presumptive midbrain4.66e-084
midbrain neural tube4.66e-084
epithelium1.89e-07174
anatomical cluster1.97e-07244
cell layer3.04e-07176
substantia nigra9.60e-073
telencephalic nucleus9.60e-073
midbrain nucleus9.60e-073
neural nucleus9.60e-073
nucleus of brain9.60e-073


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)
MA0003.10.0475636
MA0004.10.358028
MA0006.10.0376667
MA0007.10.336966
MA0009.10.425374
MA0014.10.000341065
MA0017.10.398085
MA0019.10.279241
MA0024.10.388875
MA0025.10.630472
MA0027.12.00714
MA0028.10.364782
MA0029.12.59587
MA0030.10.376415
MA0031.10.347586
MA0038.10.578883
MA0040.10.435948
MA0041.10.256066
MA0042.10.514842
MA0043.10.5085
MA0046.10.45588
MA0048.10.0168999
MA0050.10.414313
MA0051.10.593414
MA0052.10.442788
MA0055.10.0541681
MA0056.10
MA0057.10.108538
MA0058.10.231244
MA0059.10.246439
MA0060.10.0168335
MA0061.10.468254
MA0063.10
MA0066.11.06752
MA0067.10.732677
MA0068.10.796791
MA0069.10.443076
MA0070.10.434849
MA0071.10.81947
MA0072.10.427684
MA0073.10.0117568
MA0074.10.504232
MA0076.10.438642
MA0077.11.05438
MA0078.10.228674
MA0081.10.275922
MA0083.10.507806
MA0084.11.04444
MA0087.10.470385
MA0088.10.332218
MA0089.10
MA0090.10.64191
MA0091.10.376809
MA0092.10.310962
MA0093.10.381754
MA0095.10
MA0098.10
MA0100.10.161426
MA0101.10.257705
MA0103.10.188828
MA0105.10.361908
MA0106.10.66073
MA0107.10.181933
MA0108.20.296634
MA0109.10
MA0111.11.12049
MA0113.10.214338
MA0114.10.746323
MA0115.10.51095
MA0116.10.14839
MA0117.10.48285
MA0119.10.258451
MA0122.10.500096
MA0124.10.683426
MA0125.10.615761
MA0130.10
MA0131.10.27582
MA0132.10
MA0133.10
MA0135.13.37303
MA0136.10.181597
MA0139.10.302141
MA0140.10.486044
MA0141.11.223
MA0142.10.336004
MA0143.10.641011
MA0144.10.249943
MA0145.11.01256
MA0146.10.0438234
MA0147.10.11258
MA0148.10.381264
MA0149.10.0766295
MA0062.20.597388
MA0035.20.493344
MA0039.20.00121157
MA0138.20.743216
MA0002.20.153717
MA0137.20.457011
MA0104.20.175212
MA0047.20.199051
MA0112.20.763683
MA0065.21.01637
MA0150.10.10301
MA0151.10
MA0152.10.577815
MA0153.10.55531
MA0154.11.11864
MA0155.10.285814
MA0156.10.436777
MA0157.10.310784
MA0158.10
MA0159.10.29096
MA0160.10.385618
MA0161.10
MA0162.10.0318231
MA0163.10.342386
MA0164.10.181834
MA0080.20.0486268
MA0018.20.188226
MA0099.20.26517
MA0079.26.5347e-05
MA0102.21.09525
MA0258.10.691186
MA0259.10.252756
MA0442.10
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