Role for protein-protein interaction databases in human genetics

被引:38
作者
Pattin, Kristine A. [1 ]
Moore, Jason H. [1 ,2 ,3 ,4 ,5 ,6 ,7 ]
机构
[1] Dartmouth Hitchcock Med Ctr, Norris Cotton Canc Ctr, Lebanon, NH 03756 USA
[2] Dartmouth Med Sch, Computat Genet Lab, Dept Genet, Lebanon, NH USA
[3] Dartmouth Med Sch, Dept Community, Lebanon, NH USA
[4] Dartmouth Med Sch, Dept Family Med, Lebanon, NH USA
[5] Univ New Hampshire, Dept Comp Sci, Durham, NH 03824 USA
[6] Univ Vermont, Dept Comp Sci, Burlington, VT USA
[7] Translat Genom Res Inst, Phoenix, AZ USA
关键词
epistasis; expert knowledge; multifactor dimensionality reduction; protein-protein interaction; single nucleotide polymorphism; GENOME-WIDE ASSOCIATION; MULTIFACTOR-DIMENSIONALITY REDUCTION; INTERACTION NETWORK; CANDIDATE GENES; HUMAN-DISEASE; EPISTASIS; COMMON; SUSCEPTIBILITY; SEQUENCE; PATHWAYS;
D O I
10.1586/EPR.09.86
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Proteomics and the study of protein-protein interactions are becoming increasingly important in our effort to understand human diseases on a system-wide level. Thanks to the development and curation of protein-interaction databases, up-to-date information on these interaction networks is accessible and publicly available to the scientific community. As our knowledge of protein-protein interactions increases, it is important to give thought to the different ways that these resources can impact biomedical research. In this article, we highlight the importance of protein-protein interactions in human genetics and genetic epidemiology. Since protein-protein interactions demonstrate one of the strongest functional relationships between genes, combining genomic data with available proteomic data may provide us with a more in-depth understanding of common human diseases. In this review, we will discuss some of the fundamentals of protein interactions, the databases that are publicly available and how information from these databases can be used to facilitate genome-wide genetic studies.
引用
收藏
页码:647 / 659
页数:13
相关论文
共 98 条
[1]   The first genomewide interaction and locus-heterogeneity linkage scan in bipolar affective disorder:: Strong evidence of epistatic effects between loci on chromosomes 2q and 6q [J].
Abou Jamra, Rami ;
Fuerst, Robert ;
Kaneva, Radka ;
Diaz, Guillermo Orozco ;
Rivas, Fabio ;
Mayoral, Fermin ;
Gay, Eudoxia ;
Sans, Sebastian ;
Gonzalez, Maria Jose ;
Gil, Susana ;
Cabaleiro, Francisco ;
del Rio, Francisco ;
Perez, Fermin ;
Haro, Jesus ;
Auburger, Georg ;
Milanova, Vihra ;
Kostov, Christian ;
Chorbov, Vesselin ;
Stoyanova, Vessela ;
Nikolova-Hill, Amelia ;
Onchev, George ;
Kremensky, Ivo ;
Jablensky, Assen ;
Schulze, Thomas G. ;
Propping, Peter ;
Rietschel, Marcella ;
Noethen, Markus M. ;
Cichon, Sven ;
Wienker, Thomas F. ;
Schumacher, Johannes .
AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 81 (05) :974-986
[2]   The Biomolecular Interaction Network Database and related tools 2005 update [J].
Alfarano, C ;
Andrade, CE ;
Anthony, K ;
Bahroos, N ;
Bajec, M ;
Bantoft, K ;
Betel, D ;
Bobechko, B ;
Boutilier, K ;
Burgess, E ;
Buzadzija, K ;
Cavero, R ;
D'Abreo, C ;
Donaldson, I ;
Dorairajoo, D ;
Dumontier, MJ ;
Dumontier, MR ;
Earles, V ;
Farrall, R ;
Feldman, H ;
Garderman, E ;
Gong, Y ;
Gonzaga, R ;
Grytsan, V ;
Gryz, E ;
Gu, V ;
Haldorsen, E ;
Halupa, A ;
Haw, R ;
Hrvojic, A ;
Hurrell, L ;
Isserlin, R ;
Jack, F ;
Juma, F ;
Khan, A ;
Kon, T ;
Konopinsky, S ;
Le, V ;
Lee, E ;
Ling, S ;
Magidin, M ;
Moniakis, J ;
Montojo, J ;
Moore, S ;
Muskat, B ;
Ng, I ;
Paraiso, JP ;
Parker, B ;
Pintilie, G ;
Pirone, R .
NUCLEIC ACIDS RESEARCH, 2005, 33 :D418-D424
[3]   A haplotype map of the human genome [J].
Altshuler, D ;
Brooks, LD ;
Chakravarti, A ;
Collins, FS ;
Daly, MJ ;
Donnelly, P ;
Gibbs, RA ;
Belmont, JW ;
Boudreau, A ;
Leal, SM ;
Hardenbol, P ;
Pasternak, S ;
Wheeler, DA ;
Willis, TD ;
Yu, FL ;
Yang, HM ;
Zeng, CQ ;
Gao, Y ;
Hu, HR ;
Hu, WT ;
Li, CH ;
Lin, W ;
Liu, SQ ;
Pan, H ;
Tang, XL ;
Wang, J ;
Wang, W ;
Yu, J ;
Zhang, B ;
Zhang, QR ;
Zhao, HB ;
Zhao, H ;
Zhou, J ;
Gabriel, SB ;
Barry, R ;
Blumenstiel, B ;
Camargo, A ;
Defelice, M ;
Faggart, M ;
Goyette, M ;
Gupta, S ;
Moore, J ;
Nguyen, H ;
Onofrio, RC ;
Parkin, M ;
Roy, J ;
Stahl, E ;
Winchester, E ;
Ziaugra, L ;
Shen, Y .
NATURE, 2005, 437 (7063) :1299-1320
[4]   Pathways-based analyses of whole-genome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission [J].
Askland, Kathleen ;
Read, Cynthia ;
Moore, Jason .
HUMAN GENETICS, 2009, 125 (01) :63-79
[5]   Epistatic effects of polymorphisms in genes from the renin-angiotensin, bradykinin, and fibrinolytic systems on plasma t-PA and PAI-1 levels [J].
Asselbergs, Folkert W. ;
Williams, Scott M. ;
Hebert, Patricia R. ;
Coffey, Christopher S. ;
Hillege, Hans L. ;
Navis, Gerjan ;
Vaughan, Douglas E. ;
van Gilst, Wiek H. ;
Moore, Jason H. .
GENOMICS, 2007, 89 (03) :362-369
[6]  
AVERY L, 1992, TRENDS GENET, V8, P312, DOI 10.1016/0168-9525(92)90263-4
[7]  
Bateson W., 2009, Mendel's principles of heredity, V1st
[8]   From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways [J].
Bauer-Mehren, Anna ;
Furlong, Laura I. ;
Rautschka, Michael ;
Sanz, Ferran .
BMC BIOINFORMATICS, 2009, 10
[9]   The BioGRID interaction database:: 2008 update [J].
Breitkreutz, Bobby-Joe ;
Stark, Chris ;
Reguly, Teresa ;
Boucher, Lorrie ;
Breitkreutz, Ashton ;
Livstone, Michael ;
Oughtred, Rose ;
Lackner, Daniel H. ;
Bahler, Jurg ;
Wood, Valerie ;
Dolinski, Kara ;
Tyers, Mike .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D637-D640
[10]   Association between polymorphisms in RMI1, TOP3A, and BLM and risk of cancer, a case-control study [J].
Broberg, Karin ;
Huynh, Elizabeth ;
Engstrom, Karin Schlawicke ;
Bjork, Jonas ;
Albin, Maria ;
Ingvar, Christian ;
Olsson, Hakan ;
Hoglund, Mattias .
BMC CANCER, 2009, 9