From classical genetics to quantitative genetics to systems biology: Modeling epistasis

PLoS Genetics

Volumn 4, Issue 3, 2008, Pages

  Aylor, David L ^a   Zeng, Zhao Bang ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE DELETION; GENE EXPRESSION; GENE INTERACTION; GENETIC EPISTASIS; MEASUREMENT; QUANTITATIVE GENETICS; REGRESSION ANALYSIS; ALLELE; ANIMAL; BIOLOGICAL MODEL; DICTYOSTELIUM; DNA MICROARRAY; ENZYMOLOGY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; MUTATION; PHENOTYPE; SYSTEMS BIOLOGY;

CYCLIC AMP DEPENDENT PROTEIN KINASE;

ALLELES; ANIMALS; CYCLIC AMP-DEPENDENT PROTEIN KINASES; DICTYOSTELIUM; EPISTASIS, GENETIC; GENE EXPRESSION; GENE EXPRESSION PROFILING; MODELS, GENETIC; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; REGRESSION ANALYSIS; SYSTEMS BIOLOGY;

EID: 41949129310     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000029     Document Type: Article

References (26)

1. Phillips PC (1998) The language of gene interaction. Genetics 149: 1167-1171.
2. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
3. Lynch M, Walsh B (1998) Genetics and the Analysis of Quantitative Traits. Sunderland, MA: Sinauer Associates.
4. Tong AH, Lesage G, Bader GD, Ding H, Xu H, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303: 808-813.
5. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368.
6. St Onge RP, Mani R, Oh J, Proctor M, Fung E, et al. (2007) Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nat Genet 39: 199-206.
7. Jansen RC, Nap JP (2001) Genetical genomics: the added value from segregation. Trends Genet 17: 388-391.
8. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
9. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
10. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, et al. (2005) Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nat Genet 37: 225-232.
11. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, et al. (2005) Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 37: 233-242.
12. Li J, Burmeister M (2005) Genetical genomics: combining genetics with gene expression analysis. Hum Mol Genet 14 Spec No. 2: R163-169.
13. Storey JD, Akey JM, Kruglyak L (2005) Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol 3: e267.
14. Auger DL, Gray AD, Ream TS, Kato A, Coe EH Jr, et al. (2005) Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics 169: 389-397.
15. Gibson G, Riley-Berger R, Harshman L, Kopp A, Vacha S, et al. (2004) Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster. Genetics 167: 1791-1799.
16. Gibson G, Weir B (2005) The quantitative genetics of transcription. Trends Genet 21: 616-623.
17. Brem RB, Kruglyak L (2005) The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc Natl Acad Sci U S A 102: 1572-1577.
18. Avery L, Wasserman S (1992) Ordering gene function: the interpretation of epistasis in regulatory hierarchies. Trends Genet 8: 312-316.
19. Li R, Tsaih SW, Shockley K, Stylianou IM, Wergedal J, et al. (2006) Structural model analysis of multiple quantitative traits. PLoS Genet 2: e114.
20. Van Driessche N, Shaw C, Katoh M, Morio T, Sucgang R, et al. (2002) A transcriptional profile of multicellular development in Dictyostelium discoideum. Development 129: 1543-1552.
21. Van Driessche N, Demsar J, Booth EO, Hill P, Juvan P, et al. (2005) Epistasis analysis with global transcriptional phenotypes. Nat Genet 37: 471-477.
22. Souza GM, da Silva AM, Kuspa A (1999) Starvation promotes Dictyostelium development by relieving PufA inhibition of PKA translation through the YakA kinase pathway. Development 126: 3263-3274.
23. Shaulsky G, Fuller D, Loomis WF (1998) A cAMP-phosphodiesterase controls PKA-dependent differentiation. Development 125: 691-699.
24. Frankel WN, Schork NJ (1996) Who's afraid of epistasis? Nat Genet 14: 371-373.
25. Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D (2007) How to infer gene networks from expression profiles. Mol Syst Biol 3: 78.
26. R Development Core Team (2007) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing: ISBN 3-900051-07-0.