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PubMed:21972245 JSONTXT

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PubTator4TogoVar

Id Subject Object Predicate Lexical cue proteinmutation
21972245_0 676-682 ProteinMutation denotes G2019S rs34637584
21972245_1 684-690 ProteinMutation denotes G2019S rs34637584
21972245_2 895-901 ProteinMutation denotes G2019S rs34637584
21972245_3 1027-1033 ProteinMutation denotes G2019S rs34637584
21972245_4 1272-1278 ProteinMutation denotes G2019S rs34637584
21972245_5 1458-1464 ProteinMutation denotes G2019S rs34637584

c_corpus

Id Subject Object Predicate Lexical cue
T1 37-41 SO:0001742 denotes gain
T3 61-68 6308 denotes leucine
T4 61-68 SO:0001437 denotes leucine
T2 61-68 CHEBI:15603 denotes leucine
T5 61-68 D007930 denotes leucine
T6 61-68 CHEBI:25017 denotes leucine
T7 61-68 D007930 denotes leucine
T8 74-80 SO:0001068 denotes repeat
T9 91-96 PR:Q5S006 denotes LRRK2
T10 91-96 PR:000003033 denotes LRRK2
T11 91-96 PR:Q5S007 denotes LRRK2
T12 98-102 SO:0000704 denotes gene
T13 122-131 UBERON:0004529 denotes processes
T14 145-150 PR:Q5S006 denotes LRRK2
T15 145-150 PR:000003033 denotes LRRK2
T16 145-150 PR:Q5S007 denotes LRRK2
T18 178-185 6308 denotes leucine
T19 178-185 SO:0001437 denotes leucine
T17 178-185 CHEBI:15603 denotes leucine
T20 178-185 D007930 denotes leucine
T21 178-185 CHEBI:25017 denotes leucine
T22 178-185 D007930 denotes leucine
T23 191-197 SO:0001068 denotes repeat
T24 207-211 SO:0000704 denotes gene
T25 213-218 PR:Q5S006 denotes LRRK2
T26 213-218 PR:000003033 denotes LRRK2
T27 213-218 PR:Q5S007 denotes LRRK2
T32 257-276 D010300 denotes Parkinson's disease
T33 257-276 D010300 denotes Parkinson's disease
T36 297-315 C566739 denotes autosomal dominant
T37 400-405 PR:Q5S006 denotes LRRK2
T38 400-405 PR:000003033 denotes LRRK2
T39 400-405 PR:Q5S007 denotes LRRK2
T40 469-474 PR:Q5S006 denotes LRRK2
T41 469-474 PR:000003033 denotes LRRK2
T42 469-474 PR:Q5S007 denotes LRRK2
T43 522-527 PR:Q5S006 denotes LRRK2
T44 522-527 PR:000003033 denotes LRRK2
T45 522-527 PR:Q5S007 denotes LRRK2
T46 528-543 GO:0016301 denotes kinase activity
T47 564-570 SO:0001026 denotes genome
T50 576-580 SO:0000234 denotes mRNA
T48 576-580 D012333 denotes mRNA
T49 576-580 CHEBI:33699 denotes mRNA
T51 595-604 UBERON:0000955 denotes the brain
T54 633-638 PR:Q5S006 denotes LRRK2
T55 633-638 PR:000003033 denotes LRRK2
T56 633-638 PR:Q5S007 denotes LRRK2
T57 692-702 SO:0000781 denotes transgenic
T58 692-707 10090 denotes transgenic mice
T59 692-707 D008822 denotes transgenic mice
T60 703-707 PR:000005054 denotes mice
T62 703-707 O89094 denotes mice
T66 747-751 SO:0000234 denotes mRNA
T64 747-751 D012333 denotes mRNA
T65 747-751 CHEBI:33699 denotes mRNA
T67 789-798 SO:0000817 denotes wild-type
T68 820-826 UBERON:0001851 denotes cortex
T69 828-836 UBERON:0002435 denotes striatum
T70 828-836 UBERON:0005383 denotes striatum
T71 841-847 UBERON:0002113 denotes kidney
T72 879-887 UBERON:0002435 denotes striatum
T73 879-887 UBERON:0005383 denotes striatum
T74 1050-1056 UBERON:0001851 denotes cortex
T75 1058-1066 UBERON:0002435 denotes striatum
T76 1058-1066 UBERON:0005383 denotes striatum
T77 1068-1074 UBERON:0002113 denotes kidney
T78 1079-1085 UBERON:0001630 denotes muscle
T79 1079-1085 UBERON:0005090 denotes muscle
T82 1118-1122 SO:0000234 denotes mRNA
T80 1118-1122 D012333 denotes mRNA
T81 1118-1122 CHEBI:33699 denotes mRNA
T83 1253-1262 SO:0000119 denotes regulated
T84 1266-1271 PR:Q5S006 denotes LRRK2
T85 1266-1271 PR:000003033 denotes LRRK2
T86 1266-1271 PR:Q5S007 denotes LRRK2
T87 1293-1298 PR:Q5S006 denotes LRRK2
T88 1293-1298 PR:000003033 denotes LRRK2
T89 1293-1298 PR:Q5S007 denotes LRRK2
T91 1329-1337 GO:0016020 denotes membrane
T90 1329-1337 UBERON:0000094 denotes membrane
T92 1329-1337 UBERON:0000158 denotes membrane
T93 1356-1381 GO:0006119 denotes oxidative phosphorylation
T97 1383-1387 SO:0000234 denotes mRNA
T95 1383-1387 D012333 denotes mRNA
T96 1383-1387 CHEBI:33699 denotes mRNA
T98 1383-1398 GO:0006397 denotes mRNA processing
T99 1407-1428 GO:0005783 denotes endoplasmic reticulum
T100 1419-1428 UBERON:0007361 denotes reticulum
T101 1439-1448 SO:0000119 denotes regulated
T102 1452-1457 PR:Q5S006 denotes LRRK2
T103 1452-1457 PR:000003033 denotes LRRK2
T104 1452-1457 PR:Q5S007 denotes LRRK2
T106 1465-1469 D051379 denotes mice
T108 1465-1469 10095 denotes mice
T105 1465-1469 PR:000005054 denotes mice
T107 1465-1469 O89094 denotes mice
T109 1531-1536 PR:Q5S006 denotes LRRK2
T110 1531-1536 PR:000003033 denotes LRRK2
T111 1531-1536 PR:Q5S007 denotes LRRK2
T112 1537-1546 SO:0000119 denotes regulated
T113 1572-1579 SO:0001031 denotes reverse
T114 1572-1593 GO:0001171 denotes reverse transcription
T116 1605-1610 SO:0000419 denotes chain
T117 1605-1619 MOP:0000635 denotes chain reaction
T118 1723-1728 PR:Q5S006 denotes LRRK2
T119 1723-1728 PR:000003033 denotes LRRK2
T120 1723-1728 PR:Q5S007 denotes LRRK2
T121 1803-1812 CHEBI:59163 denotes biomarker
T122 1828-1833 PR:Q5S006 denotes LRRK2
T123 1828-1833 PR:000003033 denotes LRRK2
T124 1828-1833 PR:Q5S007 denotes LRRK2
T125 1883-1888 PR:Q5S006 denotes LRRK2
T126 1883-1888 PR:000003033 denotes LRRK2
T127 1883-1888 PR:Q5S007 denotes LRRK2

PubmedHPO

Id Subject Object Predicate Lexical cue
T1 257-266 HP_0001300 denotes Parkinson
T2 297-315 HP_0000006 denotes autosomal dominant
T3 664-675 HP_0000752 denotes hyperactive

Allie

Id Subject Object Predicate Lexical cue
SS1_21972245_0_0 61-89 expanded denotes leucine-rich repeat kinase 2
SS2_21972245_0_0 91-96 abbr denotes LRRK2
SS1_21972245_1_0 178-211 expanded denotes leucine-rich repeat kinase 2 gene
SS2_21972245_1_0 213-218 abbr denotes LRRK2
SS1_21972245_1_1 257-276 expanded denotes Parkinson's disease
SS2_21972245_1_1 278-280 abbr denotes PD
SS1_21972245_3_0 639-647 expanded denotes knockout
SS2_21972245_3_0 649-651 abbr denotes KO
SS1_21972245_4_0 789-798 expanded denotes wild-type
SS2_21972245_4_0 800-802 abbr denotes WT
AE1_21972245_0_0 SS1_21972245_0_0 SS2_21972245_0_0 abbreviatedTo leucine-rich repeat kinase 2,LRRK2
AE1_21972245_1_0 SS1_21972245_1_0 SS2_21972245_1_0 abbreviatedTo leucine-rich repeat kinase 2 gene,LRRK2
AE1_21972245_1_1 SS1_21972245_1_1 SS2_21972245_1_1 abbreviatedTo Parkinson's disease,PD
AE1_21972245_3_0 SS1_21972245_3_0 SS2_21972245_3_0 abbreviatedTo knockout,KO
AE1_21972245_4_0 SS1_21972245_4_0 SS2_21972245_4_0 abbreviatedTo wild-type,WT

UseCases_ArguminSci_Discourse

Id Subject Object Predicate Lexical cue
T1 0-160 DRI_Background denotes Transcriptional responses to loss or gain of function of the leucine-rich repeat kinase 2 (LRRK2) gene uncover biological processes modulated by LRRK2 activity.
T2 161-341 DRI_Approach denotes Mutations in the leucine-rich repeat kinase 2 gene (LRRK2) are the most common genetic cause of Parkinson's disease (PD) and cause both autosomal dominant familial and sporadic PD.
T3 342-428 DRI_Background denotes Currently, the physiological and pathogenic activities of LRRK2 are poorly understood.
T4 429-708 DRI_Background denotes To decipher the biological functions of LRRK2, including the genes and pathways modulated by LRRK2 kinase activity in vivo, we assayed genome-wide mRNA expression in the brain and peripheral tissues from LRRK2 knockout (KO) and kinase hyperactive G2019S (G2019S) transgenic mice.
T5 709-908 DRI_Outcome denotes Subtle but significant differences in mRNA expression were observed relative to wild-type (WT) controls in the cortex, striatum and kidney of KO animals, but only in the striatum in the G2019S model.
T6 909-1167 DRI_Background denotes In contrast, robust, consistent and highly significant differences were identified by the direct comparison of KO and G2019S profiles in the cortex, striatum, kidney and muscle, indicating opposite effects on mRNA expression by the two models relative to WT.
T7 1168-1265 DRI_Background denotes Ribosomal and glycolytic biological functions were consistently and significantly up-regulated in
T8 1266-1278 Token_Label.OUTSIDE denotes LRRK2 G2019S
T9 1279-1310 DRI_Background denotes compared with LRRK2 KO tissues.
T10 1311-1451 DRI_Background denotes Genes involved in membrane-bound organelles, oxidative phosphorylation, mRNA processing and the endoplasmic reticulum were down-regulated in
T11 1452-1464 Token_Label.OUTSIDE denotes LRRK2 G2019S
T12 1465-1487 DRI_Background denotes mice compared with KO.
T13 1488-1620 DRI_Outcome denotes We confirmed the expression patterns of 35 LRRK2-regulated genes using quantitative reverse transcription polymerase chain reaction.
T14 1621-1903 DRI_Background denotes These findings provide the first description of the transcriptional responses to genetically modified LRRK2 activity and provide preclinical target engagement and/or pharmacodynamic biomarker strategies for LRRK2 and may inform future therapeutic strategies for LRRK2-associated PD.

PubMed_ArguminSci

Id Subject Object Predicate Lexical cue
T1 161-341 DRI_Approach denotes Mutations in the leucine-rich repeat kinase 2 gene (LRRK2) are the most common genetic cause of Parkinson's disease (PD) and cause both autosomal dominant familial and sporadic PD.
T2 342-428 DRI_Background denotes Currently, the physiological and pathogenic activities of LRRK2 are poorly understood.
T3 429-708 DRI_Background denotes To decipher the biological functions of LRRK2, including the genes and pathways modulated by LRRK2 kinase activity in vivo, we assayed genome-wide mRNA expression in the brain and peripheral tissues from LRRK2 knockout (KO) and kinase hyperactive G2019S (G2019S) transgenic mice.
T4 709-908 DRI_Outcome denotes Subtle but significant differences in mRNA expression were observed relative to wild-type (WT) controls in the cortex, striatum and kidney of KO animals, but only in the striatum in the G2019S model.
T5 909-1167 DRI_Background denotes In contrast, robust, consistent and highly significant differences were identified by the direct comparison of KO and G2019S profiles in the cortex, striatum, kidney and muscle, indicating opposite effects on mRNA expression by the two models relative to WT.
T6 1168-1265 DRI_Background denotes Ribosomal and glycolytic biological functions were consistently and significantly up-regulated in
T7 1279-1310 DRI_Background denotes compared with LRRK2 KO tissues.
T8 1311-1451 DRI_Background denotes Genes involved in membrane-bound organelles, oxidative phosphorylation, mRNA processing and the endoplasmic reticulum were down-regulated in
T9 1465-1487 DRI_Background denotes mice compared with KO.
T10 1488-1620 DRI_Outcome denotes We confirmed the expression patterns of 35 LRRK2-regulated genes using quantitative reverse transcription polymerase chain reaction.
T11 1621-1903 DRI_Background denotes These findings provide the first description of the transcriptional responses to genetically modified LRRK2 activity and provide preclinical target engagement and/or pharmacodynamic biomarker strategies for LRRK2 and may inform future therapeutic strategies for LRRK2-associated PD.

DisGeNET5_variant_disease

Id Subject Object Predicate Lexical cue
21972245-3#247#253#geners34637584 676-682 geners34637584 denotes G2019S
21972245-3#255#261#geners34637584 684-690 geners34637584 denotes G2019S
21972245-3#235#246#diseaseC0424295 664-675 diseaseC0424295 denotes hyperactive
247#253#geners34637584235#246#diseaseC0424295 21972245-3#247#253#geners34637584 21972245-3#235#246#diseaseC0424295 associated_with G2019S,hyperactive
255#261#geners34637584235#246#diseaseC0424295 21972245-3#255#261#geners34637584 21972245-3#235#246#diseaseC0424295 associated_with G2019S,hyperactive

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
21972245-3#40#45#gene120892 469-474 gene120892 denotes LRRK2
21972245-3#93#98#gene120892 522-527 gene120892 denotes LRRK2
21972245-3#204#209#gene120892 633-638 gene120892 denotes LRRK2
21972245-3#235#246#diseaseC0424295 664-675 diseaseC0424295 denotes hyperactive
21972245-9#102#107#gene120892 1723-1728 gene120892 denotes LRRK2
21972245-9#207#212#gene120892 1828-1833 gene120892 denotes LRRK2
21972245-9#262#267#gene120892 1883-1888 gene120892 denotes LRRK2
21972245-9#279#281#diseaseC0030567 1900-1902 diseaseC0030567 denotes PD
40#45#gene120892235#246#diseaseC0424295 21972245-3#40#45#gene120892 21972245-3#235#246#diseaseC0424295 associated_with LRRK2,hyperactive
93#98#gene120892235#246#diseaseC0424295 21972245-3#93#98#gene120892 21972245-3#235#246#diseaseC0424295 associated_with LRRK2,hyperactive
204#209#gene120892235#246#diseaseC0424295 21972245-3#204#209#gene120892 21972245-3#235#246#diseaseC0424295 associated_with LRRK2,hyperactive
102#107#gene120892279#281#diseaseC0030567 21972245-9#102#107#gene120892 21972245-9#279#281#diseaseC0030567 associated_with LRRK2,PD
207#212#gene120892279#281#diseaseC0030567 21972245-9#207#212#gene120892 21972245-9#279#281#diseaseC0030567 associated_with LRRK2,PD
262#267#gene120892279#281#diseaseC0030567 21972245-9#262#267#gene120892 21972245-9#279#281#diseaseC0030567 associated_with LRRK2,PD