title: Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer.
abstract: Mammalian cells have cytoplasmic and mitochondrial aminoacyl-tRNA synthetases (ARSs) that catalyze aminoacylation of tRNAs during protein synthesis. Despite their housekeeping functions in protein synthesis, recently, ARSs and ARS-interacting multifunctional proteins (AIMPs) have been shown to play important roles in disease pathogenesis through their interactions with disease-related molecules. However, there are lacks of data resources and analytical tools that can be used to examine disease associations of ARS/AIMPs. Here, we developed an Integrated Database for ARSs (IDA), a resource database including cancer genomic/proteomic and interaction data of ARS/AIMPs. IDA includes mRNA expression, somatic mutation, copy number variation and phosphorylation data of ARS/AIMPs and their interacting proteins in various cancers. IDA further includes an array of analytical tools for exploration of disease association of ARS/AIMPs, identification of disease-associated ARS/AIMP interactors and reconstruction of ARS-dependent disease-perturbed network models. Therefore, IDA provides both comprehensive data resources and analytical tools for understanding potential roles of ARS/AIMPs in cancers.
authors.affiliation: Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Ji-Hyun
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Sungyong
authors.initials: S
authors.lastname: You
authors.affiliation: Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Do Young
authors.initials: do Y
authors.lastname: Hyeon
authors.affiliation: Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Byeongsoo
authors.initials: B
authors.lastname: Kang
authors.affiliation: Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Hyerim
authors.initials: H
authors.lastname: Kim
authors.affiliation: Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Kyoung Mii
authors.initials: KM
authors.lastname: Park
authors.affiliation: Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Byungwoo
authors.initials: B
authors.lastname: Han
authors.affiliation: Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea dhwang@dgist.ac.kr.
authors.forename: Daehee
authors.initials: D
authors.lastname: Hwang
authors.affiliation: Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea Medicinal Bioconvergence Research Center and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea, School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Republic of Korea, Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea and Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea sungkim@snu.ac.kr.
authors.forename: Sunghoon
authors.initials: S
authors.lastname: Kim
mesh_terms: D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics / Q000378:metabolism; D030562:Databases, Protein; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008954:Models, Biological; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000378:metabolism; D040901:Proteomics
chemical_list: D009363:Neoplasm Proteins; D020543:Proteome; D000604:Amino Acyl-tRNA Synthetases
references.citation: Sci Signal. 2013 Feb 26;6(264):rs4
references.pmid: 23443683
references.citation: Mol Cell. 2009 Jul 31;35(2):164-80
references.pmid: 19647514
references.citation: BMC Bioinformatics. 2009;10:307
references.pmid: 19775443
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22
references.pmid: 18981052
references.citation: Nucleic Acids Res. 2013 Jan 7;41(1):667-76
references.pmid: 23161686
references.citation: IUBMB Life. 2010 Apr;62(4):296-302
references.pmid: 20306515
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):248-50
references.pmid: 12519993
references.citation: Cell. 2011 Oct 28;147(3):690-703
references.pmid: 22036573
references.citation: Cell. 2000 Jun 9;101(6):573-6
references.pmid: 10892642
references.citation: J Biol Chem. 2006 Dec 15;281(50):38663-7
references.pmid: 17062567
references.citation: Science. 2003 Apr 18;300(5618):445-52
references.pmid: 12702867
references.citation: Mol Syst Biol. 2008;4:218
references.pmid: 18766178
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D830-5
references.pmid: 17932056
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D885-90
references.pmid: 18940857
references.citation: Am J Hum Genet. 2008 Apr;82(4):949-58
references.pmid: 18371930
references.citation: Nat Cell Biol. 2004 Feb;6(2):97-105
references.pmid: 14743216
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
references.pmid: 16381927
references.citation: EMBO Mol Med. 2013 Mar;5(3):332-43
references.pmid: 23427196
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: Genome Biol. 2007;8(5):R95
references.pmid: 17535438
references.citation: Top Curr Chem. 2014;344:119-44
references.pmid: 24072587
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5
references.pmid: 17145710
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D651-6
references.pmid: 18988626
references.citation: Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15084-9
references.pmid: 25288775
references.citation: Nat Methods. 2011 Jul;8(7):528-9
references.pmid: 21716279
references.citation: J Biol Chem. 2008 Oct 17;283(42):28321-8
references.pmid: 18715867
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D945-50
references.pmid: 20952405
references.citation: Bioinformatics. 2003 Jan 22;19(2):185-93
references.pmid: 12538238
references.citation: Nature. 2014 Mar 20;507(7492):315-22
references.pmid: 24476821
references.citation: Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11206-11
references.pmid: 18695251
references.citation: Anticancer Res. 2012 Jan;32(1):73-9
references.pmid: 22213290
references.citation: Bioinformatics. 2005 May 1;21(9):2076-82
references.pmid: 15657099
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):289-91
references.pmid: 10592249
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4
references.pmid: 17135203
references.citation: Mol Cell. 2014 Dec 18;56(6):763-76
references.pmid: 25453761
references.citation: Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6164-9
references.pmid: 9177188
references.citation: Nucleic Acids Res. 2000 Sep 15;28(18):3442-4
references.pmid: 10982861
references.citation: BMC Cancer. 2014;14:620
references.pmid: 25163878
references.citation: Nature. 2010 Feb 18;463(7283):899-905
references.pmid: 20164920
references.citation: BMC Syst Biol. 2012;6:80
references.pmid: 22748168
references.citation: Cancer Res. 2006 Jul 15;66(14):6913-8
references.pmid: 16849534
references.citation: Proteomics. 2004 Jun;4(6):1551-61
references.pmid: 15174125
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D964-71
references.pmid: 22096234
references.citation: J Biol Chem. 2010 Mar 19;285(12):9262-72
references.pmid: 20071342
references.citation: FASEB J. 2012 Oct;26(10):4142-59
references.pmid: 22751010
references.citation: Gut Liver. 2010 Sep;4(3):430-1
references.pmid: 20981229
references.citation: N Engl J Med. 2013 May 30;368(22):2059-74
references.pmid: 23634996
references.citation: Nat Rev Cancer. 2011 Oct;11(10):708-18
references.pmid: 21941282
references.citation: Ann Surg Oncol. 2014 Jun;21(6):2020-7
references.pmid: 24558064
references.citation: Nature. 2012 Mar 29;483(7391):603-7
references.pmid: 22460905
references.citation: Nature. 2012 Oct 4;490(7418):61-70
references.pmid: 23000897
references.citation: Trends Biochem Sci. 2005 Oct;30(10):569-74
references.pmid: 16125937
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D497-501
references.pmid: 14681466
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D253-60
references.pmid: 21081558
references.citation: Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11043-9
references.pmid: 18682559
references.citation: Proc Natl Acad Sci U S A. 2005 May 3;102(18):6356-61
references.pmid: 15851690
references.citation: Nat Genet. 1997 Jan;15(1):91-4
references.pmid: 8988176
references.citation: Nat Biotechnol. 2005 Aug;23(8):951-9
references.pmid: 16082366
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9
references.pmid: 22096231
references.citation: Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17296-301
references.pmid: 16301537
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D747-50
references.pmid: 17132828
references.citation: Nucleic Acids Res. 1999 Jan 1;27(1):29-34
references.pmid: 9847135
references.citation: PLoS Genet. 2011 Mar;7(3):e1001351
references.pmid: 21483803
references.citation: Carcinogenesis. 2009 Sep;30(9):1638-44
references.pmid: 19622630
references.citation: Nature. 2012 Jul 19;487(7407):330-7
references.pmid: 22810696
references.citation: Nature. 2012 Sep 27;489(7417):519-25
references.pmid: 22960745
references.citation: Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):E640-7
references.pmid: 22345558
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011