A computational system to select candidate genes for complex human traits

被引：59

作者：

Gaulton, Kyle J. ^{[1
]}

Mohlke, Karen L.

Vision, Todd J.

机构：

[1] Univ N Carolina, Curriculum Genet & Mol Biol, Chapel Hill, NC 27516 USA

[2] Univ N Carolina, Dept Genet, Chapel Hill, NC 27516 USA

[3] Univ N Carolina, Dept Biol, Chapel Hill, NC 27516 USA

来源：

BIOINFORMATICS | 2007年 / 23卷 / 09期

关键词：

D O I：

10.1093/bioinformatics/btm001

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Identification of the genetic variation underlying complex traits is challenging. The wealth of information publicly available about the biology of complex traits and the function of individual genes permits the development of informatics-assisted methods for the selection of candidate genes for these traits. Results: We have developed a computational system named CAESAR that ranks all annotated human genes as candidates for a complex trait by using ontologies to semantically map natural language descriptions of the trait with a variety of gene-centric information sources. In a test of its effectiveness, CAESAR successfully selected 7 out of 18 (39%) complex human trait susceptibility genes within the top 2% of ranked candidates genome-wide, a subset that represents roughly 1% of genes in the human genome and provides sufficient enrichment for an association study of several hundred human genes. This approach can be applied to any well-documented mono- or multi-factorial trait in any organism for which an annotated gene set exists.

引用

页码：1132 / 1140

页数：9

共 45 条

[1] SUSPECTS: enabling fast and effective prioritization of positional candidates [J].

Adie, EA ;

Adams, RR ;

Evans, KL ;

Porteous, DJ ;

Pickard, BS .

BIOINFORMATICS, 2006, 22 (06) :773-774

[2] Gene prioritization through genomic data fusion [J].

Aerts, S ;

Lambrechts, D ;

Maity, S ;

Van Loo, P ;

Coessens, B ;

De Smet, F ;

Tranchevent, LC ;

De Moor, B ;

Marynen, P ;

Hassan, B ;

Carmeliet, P ;

Moreau, Y .

NATURE BIOTECHNOLOGY, 2006, 24 (05) :537-544

[3] 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

[4] InterPro - an integrated documentation resource for protein families, domains and functional sites [J].

Apweiler, R ;

Attwood, TK ;

Bairoch, A ;

Bateman, A ;

Birney, E ;

Biswas, M ;

Bucher, P ;

Cerutti, L ;

Corpet, F ;

Croning, MDR ;

Durbin, R ;

Falquet, L ;

Fleischmann, W ;

Gouzy, J ;

Hermjakob, H ;

Hulo, N ;

Jonassen, I ;

Kahn, D ;

Kanapin, A ;

Karavidopoulou, Y ;

Lopez, R ;

Marx, B ;

Mulder, NJ ;

Oinn, TM ;

Pagni, M ;

Servant, F ;

Sigrist, CJA ;

Zdobnov, EM .

BIOINFORMATICS, 2000, 16 (12) :1145-1150

[5] The universal protein resource (UniProt) [J].

Bairoch, A ;

Apweiler, R ;

Wu, CH ;

Barker, WC ;

Boeckmann, B ;

Ferro, S ;

Gasteiger, E ;

Huang, HZ ;

Lopez, R ;

Magrane, M ;

Martin, MJ ;

Natale, DA ;

O'Donovan, C ;

Redaschi, N ;

Yeh, LSL .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D154-D159

[6]

Becker KG, 2004, NAT GENET, V36, P431, DOI 10.1038/ng0504-431

[7] A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis [J].

Begovich, AB ;

Carlton, VEH ;

Honigberg, LA ;

Schrodi, SJ ;

Chokkalingam, AP ;

Alexander, HC ;

Ardlie, KG ;

Huang, QQ ;

Smith, AM ;

Spoerke, JM ;

Conn, MT ;

Chang, M ;

Chang, SYP ;

Saiki, RK ;

Catanese, JJ ;

Leong, DU ;

Garcia, VE ;

McAllister, LB ;

Jeffery, DA ;

Lee, AT ;

Batliwalla, F ;

Remmers, E ;

Criswell, LA ;

Seldin, MF ;

Kastner, DL ;

Amos, CI ;

Sninsky, JJ ;

Gregersen, PK .

AMERICAN JOURNAL OF HUMAN GENETICS, 2004, 75 (02) :330-337

[8] Ensembl 2006 [J].

Birney, E. ;

Andrews, D. ;

Caccamo, M. ;

Chen, Y. ;

Clarke, L. ;

Coates, G. ;

Cox, T. ;

Cunningham, F. ;

Curwen, V. ;

Cutts, T. ;

Down, T. ;

Durbin, R. ;

Fernandez-Suarez, X. M. ;

Flicek, P. ;

Graf, S. ;

Hammond, M. ;

Herrero, J. ;

Howe, K. ;

Iyer, V. ;

Jekosch, K. ;

Kahari, A. ;

Kasprzyk, A. ;

Keefe, D. ;

Kokocinski, F. ;

Kulesha, E. ;

London, D. ;

Longden, I. ;

Melsopp, C. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Proctor, G. ;

Prlic, A. ;

Rae, M. ;

Rios, D. ;

Redmond, S. ;

Schuster, M. ;

Sealy, I. ;

Searle, S. ;

Severin, J. ;

Slater, G. ;

Smedley, D. ;

Smith, J. ;

Stabenau, A. ;

Stalker, J. ;

Trevanion, S. ;

Ureta-Vidal, A. ;

Vogel, J. ;

White, S. ;

Woodwark, C. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D556-D561

[9] MGD: the Mouse Genome Database [J].

Blake, JA ;

Richardson, JE ;

Bult, RJ ;

Kadin, JA ;

Eppig, JT .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :193-195

[10] A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes [J].

Bottini, N ;

Musumeci, L ;

Alonso, A ;

Rahmouni, S ;

Nika, K ;

Rostamkhani, M ;

MacMurray, J ;

Meloni, GF ;

Lucarelli, P ;

Pellecchia, M ;

Eisenbarth, GS ;

Comings, D ;

Mustelin, T .

NATURE GENETICS, 2004, 36 (04) :337-338

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