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

[21] The Gene Ontology (GO) database and informatics resource [J].

Harris, MA ;

Clark, J ;

Ireland, A ;

Lomax, J ;

Ashburner, M ;

Foulger, R ;

Eilbeck, K ;

Lewis, S ;

Marshall, B ;

Mungall, C ;

Richter, J ;

Rubin, GM ;

Blake, JA ;

Bult, C ;

Dolan, M ;

Drabkin, H ;

Eppig, JT ;

Hill, DP ;

Ni, L ;

Ringwald, M ;

Balakrishnan, R ;

Cherry, JM ;

Christie, KR ;

Costanzo, MC ;

Dwight, SS ;

Engel, S ;

Fisk, DG ;

Hirschman, JE ;

Hong, EL ;

Nash, RS ;

Sethuraman, A ;

Theesfeld, CL ;

Botstein, D ;

Dolinski, K ;

Feierbach, B ;

Berardini, T ;

Mundodi, S ;

Rhee, SY ;

Apweiler, R ;

Barrell, D ;

Camon, E ;

Dimmer, E ;

Lee, V ;

Chisholm, R ;

Gaudet, P ;

Kibbe, W ;

Kishore, R ;

Schwarz, EM ;

Sternberg, P ;

Gwinn, M .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D258-D261

[22] A variant of the gene encoding leukotriene A4 hydrolase confers ethnicity-specific risk of myocardial infarction [J].

Helgadottir, A ;

Manolescu, A ;

Helgason, A ;

Thorleifsson, G ;

Thorsteinsdottir, U ;

Gudbjartsson, DF ;

Gretarsdottir, S ;

Magnusson, KP ;

Gudmundsson, G ;

Hicks, A ;

Jonsson, T ;

Grant, SFA ;

Sainz, J ;

O'Brien, SJ ;

Sveinbjornsdottir, S ;

Valdimarsson, EM ;

Matthiasson, SE ;

Levey, AI ;

Abramson, JL ;

Reilly, MP ;

Vaccarino, V ;

Wolfe, ML ;

Gudnason, V ;

Quyyumi, AA ;

Topol, EJ ;

Rader, DJ ;

Thorgeirsson, G ;

Gulcher, JR ;

Hakonarson, H ;

Kong, A ;

Stefansson, K .

NATURE GENETICS, 2006, 38 (01) :68-74

[23] Overview of BioCreAtIvE task IB: normalized gene lists [J].

Hirschman, L ;

Colosimo, M ;

Morgan, A ;

Yeh, A .

BMC BIOINFORMATICS, 2005, 6 (Suppl 1)

[24] The KEGG resource for deciphering the genome [J].

Kanehisa, M ;

Goto, S ;

Kawashima, S ;

Okuno, Y ;

Hattori, M .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D277-D280

[25] eVOC: A controlled vocabulary for unifying gene expression data [J].

Kelso, J ;

Visagie, J ;

Theiler, G ;

Christoffels, A ;

Bardien, S ;

Smedley, D ;

Otgaar, D ;

Greyling, G ;

Jongeneel, CV ;

McCarthy, MI ;

Hide, T ;

Hide, W .

GENOME RESEARCH, 2003, 13 (06) :1222-1230

[26] Complement factor H polymorphism in age-related macular degeneration [J].

Klein, RJ ;

Zeiss, C ;

Chew, EY ;

Tsai, JY ;

Sackler, RS ;

Haynes, C ;

Henning, AK ;

SanGiovanni, JP ;

Mane, SM ;

Mayne, ST ;

Bracken, MB ;

Ferris, FL ;

Ott, J ;

Barnstable, C ;

Hoh, J .

SCIENCE, 2005, 308 (5720) :385-389

[27] A functional variant in FCRL3, encoding Fc receptor-like 3, is associated with rheumatoid arthritis and several autoimmunities [J].

Kochi, Y ;

Yamada, R ;

Suzuki, A ;

Harley, JB ;

Shirasawa, S ;

Sawada, T ;

Bae, SC ;

Tokuhiro, S ;

Chang, XT ;

Sekine, A ;

Takahashi, A ;

Tsunoda, T ;

Ohnishi, Y ;

Kaufman, KM ;

Kang, CSP ;

Kang, CW ;

Otsubo, S ;

Yumura, W ;

Mimori, A ;

Koike, T ;

Nakamura, Y ;

Sasazuki, T ;

Yamamoto, K .

NATURE GENETICS, 2005, 37 (05) :478-485

[28] Characterization of a common susceptibility locus for asthma-related traits [J].

Laitinen, T ;

Polvi, A ;

Rydman, P ;

Vendelin, J ;

Pulkkinen, V ;

Salmikangas, P ;

Mäkelä, S ;

Rehn, M ;

Pirskanen, A ;

Rautanen, A ;

Zucchelli, M ;

Gullstén, H ;

Leino, M ;

Alenius, H ;

Petäys, T ;

Haahtela, T ;

Laitinen, A ;

Laprise, C ;

Hudson, TJ ;

Laitinen, LA ;

Kere, J .

SCIENCE, 2004, 304 (5668) :300-304

[29] Entrez Gene: gene-centered information at NCBI [J].

Maglott, D ;

Ostell, J ;

Pruitt, KD ;

Tatusova, T .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D54-D58

[30] High-resolution whole-genome association study of Parkinson disease [J].

Maraganore, DM ;

de Andrade, M ;

Lesnick, TG ;

Strain, KJ ;

Farrer, MJ ;

Rocca, WA ;

Pant, PVK ;

Frazer, KA ;

Cox, DR ;

Ballinger, DG .

AMERICAN JOURNAL OF HUMAN GENETICS, 2005, 77 (05) :685-693

← 1 2 3 4 5 →