Genetic Interaction Networks: Toward an Understanding of Heritability

被引:84
作者
Baryshnikova, Anastasia [1 ]
Costanzo, Michael [2 ]
Myers, Chad L. [3 ]
Andrews, Brenda [2 ,4 ]
Boone, Charles [2 ,4 ]
机构
[1] Princeton Univ, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA
[2] Univ Toronto, Donnelly Ctr Cellular & Biomol Res, Banting & Best Dept Med Res, Toronto, ON M5S 3E1, Canada
[3] Univ Minnesota, Dept Comp Sci & Engn, Minneapolis, MN 55455 USA
[4] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 3E1, Canada
来源
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, VOL 14 | 2013年 / 14卷
基金
加拿大健康研究院;
关键词
epistasis; genetic networks; genotype-to-phenotype relationship; Saccharomyces cerevisiae; SYNTHETIC LETHAL INTERACTIONS; FUNCTIONAL-ORGANIZATION; QUANTITATIVE-ANALYSIS; PHEROMONE RESPONSE; HIGH-THROUGHPUT; INTERACTION MAP; REVEALS LINKS; YEAST; FITNESS; EXPLORATION;
D O I
10.1146/annurev-genom-082509-141730
中图分类号
Q3 [遗传学];
学科分类号
071007 [遗传学];
摘要
Understanding the relationship between the genotypes and phenotypes of individuals is key for identifying genetic variants responsible for disease and developing successful therapeutic strategies. Mapping the phenotypic effects of individual genetic variants and their combinations in human populations presents numerous practical and statistical challenges. However, model organisms, such as the budding yeast Saccharomyces cerevisiae, provide an incredible set of molecular tools and advanced technologies that should be able to efficiently perform this task. In particular, large-scale genetic interaction screens in yeast and other model systems have revealed common properties of genetic interaction networks, many of which appear to be maintained over extensive evolutionary distances. Indeed, despite relatively low conservation of individual genes and their pairwise interactions, the overall topology of genetic interaction networks and the connections between broad biological processes may be similar in most organisms. Taking advantage of these general principles should provide a fundamental basis for mapping and predicting genetic interaction networks in humans.
引用
收藏
页码:111 / 133
页数:23
相关论文
共 104 条
[1]
A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking [J].
Aguilar, Pablo S. ;
Froehlich, Florian ;
Rehman, Michael ;
Shales, Mike ;
Ulitsky, Igor ;
Olivera-Couto, Agustina ;
Braberg, Hannes ;
Shamir, Ron ;
Walter, Peter ;
Mann, Matthias ;
Ejsing, Christer S. ;
Krogan, Nevan J. ;
Walther, Tobias C. .
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2010, 17 (07) :901-U175
[2]
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants:: the Keio collection [J].
Baba, Tomoya ;
Ara, Takeshi ;
Hasegawa, Miki ;
Takai, Yuki ;
Okumura, Yoshiko ;
Baba, Miki ;
Datsenko, Kirill A. ;
Tomita, Masaru ;
Wanner, Barry L. ;
Mori, Hirotada .
MOLECULAR SYSTEMS BIOLOGY, 2006, 2 (1) :2006.0008
[3]
Functional maps of protein complexes from quantitative genetic interaction data [J].
Bandyopadhyay, Sourav ;
Kelley, Ryan ;
Krogan, Nevan J. ;
Ideker, Trey .
PLOS COMPUTATIONAL BIOLOGY, 2008, 4 (04)
[4]
Rewiring of Genetic Networks in Response to DNA Damage [J].
Bandyopadhyay, Sourav ;
Mehta, Monika ;
Kuo, Dwight ;
Sung, Min-Kyung ;
Chuang, Ryan ;
Jaehnig, Eric J. ;
Bodenmiller, Bernd ;
Licon, Katherine ;
Copeland, Wilbert ;
Shales, Michael ;
Fiedler, Dorothea ;
Dutkowski, Janusz ;
Guenole, Aude ;
van Attikum, Haico ;
Shokat, Kevan M. ;
Kolodner, Richard D. ;
Huh, Won-Ki ;
Aebersold, Ruedi ;
Keogh, Michael-Christopher ;
Krogan, Nevan J. ;
Ideker, Trey .
SCIENCE, 2010, 330 (6009) :1385-1389
[5]
Network biology:: Understanding the cell's functional organization [J].
Barabási, AL ;
Oltvai, ZN .
NATURE REVIEWS GENETICS, 2004, 5 (02) :101-U15
[6]
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale [J].
Baryshnikova, Anastasia ;
Costanzo, Michael ;
Kim, Yungil ;
Ding, Huiming ;
Koh, Judice ;
Toufighi, Kiana ;
Youn, Ji-Young ;
Ou, Jiongwen ;
San Luis, Bryan-Joseph ;
Bandyopadhyay, Sunayan ;
Hibbs, Matthew ;
Hess, David ;
Gingras, Anne-Claude ;
Bader, Gary D. ;
Troyanskaya, Olga G. ;
Brown, Grant W. ;
Andrews, Brenda ;
Boone, Charles ;
Myers, Chad L. .
NATURE METHODS, 2010, 7 (12) :1017-U110
[7]
SYNTHETIC GENETIC ARRAY (SGA) ANALYSIS IN SACCHAROMYCES CEREVISIAE AND SCHIZOSACCHAROMYCES POMBE [J].
Baryshnikova, Anastasia ;
Costanzo, Michael ;
Dixon, Scott ;
Vizeacoumar, Franco J. ;
Myers, Chad L. ;
Andrews, Brenda ;
Boone, Charles .
METHODS IN ENZYMOLOGY, VOL 470: GUIDE TO YEAST GENETICS:: FUNCTIONAL GENOMICS, PROTEOMICS, AND OTHER SYSTEMS ANALYSIS, 2ND EDITION, 2010, 470 :145-179
[8]
Putting genetic interactions in context through a global modular decomposition [J].
Bellay, Jeremy ;
Atluri, Gowtham ;
Sing, Tina L. ;
Toufighi, Kiana ;
Costanzo, Michael ;
Ribeiro, Philippe Souza Moraes ;
Pandey, Gaurav ;
Baller, Joshua ;
VanderSluis, Benjamin ;
Michaut, Magali ;
Han, Sangjo ;
Kim, Philip ;
Brown, Grant W. ;
Andrews, Brenda J. ;
Boone, Charles ;
Kumar, Vipin ;
Myers, Chad L. .
GENOME RESEARCH, 2011, 21 (08) :1375-1387
[9]
Comparative Interaction Networks: Bridging Genotype to Phenotype [J].
Beltrao, Pedro ;
Ryan, Colm ;
Krogan, Nevan J. .
EVOLUTIONARY SYSTEMS BIOLOGY, 2012, 751 :139-156
[10]
Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae [J].
Ben-Aroya, Shay ;
Coombes, Candice ;
Kwok, Teresa ;
O'Donnell, Kathryn A. ;
Boeke, Jef D. ;
Hieter, Philip .
MOLECULAR CELL, 2008, 30 (02) :248-258