Genome-Wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices

PLoS ONE

Volumn 5, Issue 7, 2010, Pages

  Eronen, Ville Pekka ^a   Lindén, Rolf O ^a   Lindroos, Anna ^a   Kanerva, Mirella ^a   Aittokallio, Tero ^a  

^a UNIVERSITY OF TURKU   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DATA MINING; GENE INTERACTION; GENE MAPPING; GENE MUTATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC EPISTASIS; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; PREDICTION; QUANTITATIVE ANALYSIS; SCORING SYSTEM; YEAST; BIOLOGY; GENETICS; METHODOLOGY;

COMPUTATIONAL BIOLOGY; EPISTASIS, GENETIC;

EID: 77955363536     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011611     Document Type: Article

References (62)

1. Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C (2009) Systematic mapping of genetic interaction networks. Annu Rev Genet 43: 601-25.
2. 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.
3. Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, et al. (2004) A robust toolkit for functional profiling of the yeast genome. Mol Cell 16: 487-496.
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. Davierwala AP,Haynes J, Li Z, Brost RL, RobinsonMD, et al. (2005) The synthetic genetic interaction spectrum of essential genes. Nat Genet 37: 1147-1152.
6. Pan X, Ye P, Yuan DS, Wang X, Bader JS, et al. (2006) A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124: 1069-1081.
7. Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, et al. (2006) Global syntheticlethality analysis and yeast functional profiling. Trends Genet 22: 56-63.
8. Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, et al. (2005) Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123: 507-519.
9. Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, et al. (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446: 806-810.
10. Decourty L, Saveanu C, Zemam K, Hantraye F, Frachon E, et al. (2008) Linking functionally related genes by sensitive and quantitative characterization of genetic interaction profiles. Proc Natl Acad Sci U S A 105: 5821-5826.
11. Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, et al. (2009) Functional organization of the S. cerevisiae phosphorylation network. Cell 136: 952-963.
12. Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, et al. (2010) The genetic landscape of a cell. Science 327: 425-431.
13. Hartman JL, Garvik B, Hartwell L (2001) Principles for the buffering of genetic variation. Science 291: 1001-1004.
14. Boone C, Bussey H, Andrews BJ (2007) Exploring genetic interactions and networks with yeast. Nat Rev Genet 8: 437-449.
15. Lehner B (2007) Modelling genotype-phenotype relationships and human disease with genetic interaction networks. J Exp Biol 210: 1559-1566.
16. Phillips PC (2008) Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9: 855-867.
17. Wong SL, Zhang LV, Tong AH, Li Z, Goldberg DS, et al. (2004) Combining biological networks to predict genetic interactions. Proc Natl Acad Sci USA 101: 15682-15687.
18. Ye P, Peyser BD, Pan X, Boeke JD, Spencer FA, et al. (2005) Gene function prediction from congruent synthetic lethal interactions in yeast. Mol Syst Biol 1: 26.
19. Ye P, Peyser BD, Spencer FA, Bader JS (2005) Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast. BMC Bioinformatics 6: 270.
20. Qi Y, Ye P, Bader JS (2005) Genetic Interaction Motif Finding by expectation maximization: a novel statistical model for inferring gene modules from synthetic lethality. BMC Bioinformatics 6: 288.
21. Zhang LV, King OD, Wong SL, Goldberg DS, Tong AH, et al. (2005) Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol 4: 6.
22. Kelley R, Ideker T (2005) Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol 23: 561-566.
23. Ulitsky I, Shamir R (2007) Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. Mol Syst Biol 3: 104.
24. Ma X, Tarone AM, Li W (2008) Mapping genetically compensatory pathways from synthetic lethal interactions in yeast. PLoS One 3: e1922.
25. Dror O, Schneidman-Duhovny D, Shulman-Peleg A, Nussinov R, Wolfson HJ, et al. (2008) Structural similarity of genetically interacting proteins. BMC Syst Biol 2: 69.
26. Le Meur N, Gentleman R (2008) Modeling synthetic lethality. Genome Biol 9: R135.
27. Paladugu SR, Zhao S, Ray A, Raval A (2008) Mining protein networks for synthetic genetic interactions. BMC Bioinformatics 9: 426.
28. Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS (2008) Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res 18: 1991-2004.
29. Chipman KC, Singh AK (2009) Predicting genetic interactions with random walks on biological networks. BMC Bioinformatics 10: 17.
30. Pan X, Yuan DS, Ooi SL, Wang X, Sookhai-Mahadeo S, et al. (2006) dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods 41: 206-221.
31. Collins SR, Schuldiner M, Krogan NJ, Weissman JS (2006) A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol 7: R63.
32. Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, et al. (2010) DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res 38: D502-D507.
33. Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T (2008) Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol 4: e1000065.
34. Ulitsky I, Shlomi T, Kupiec M, Shamir R (2008) From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol 4: 209.
35. Pu S, Ronen K, Vlasblom J, Greenblatt J, Wodak SJ (2008) Local coherence in genetic interaction patterns reveals prevalent functional versatility. Bioinformatics 24: 2376-2383.
36. Casey FP, Cagney G, Krogan NJ, Shields DC. Optimal stepwise experimental design for pairwise functional interaction studies. Bioinformatics 24: 2733-2739.
37. Ulitsky I, Krogan NJ, Shamir R (2009) Towards accurate imputation of quantitative genetic interactions. Genome Biol 10: R140.
38. Breker M, Schuldiner M (2009) Explorations in topology-delving underneath the surface of genetic interaction maps. Mol Biosyst 5: 1473-1481.
39. Beyer A, Bandyopadhyay S, Ideker T (2007) Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet 8: 699-710.
40. Drees BL, Thorsson V, Carter GW, Rives AW, Raymond MZ, et al. (2005) Derivation of genetic interaction networks from quantitative phenotype data. Genome Biol 6: R38.
41. Carter GW, Galas DJ, Galitski T (2009) Maximal extraction of biological information from genetic interaction data. PLoS Comput Biol 5: e1000347.
42. Mani R, St Onge RP, Hartman JL, Giaever G, Roth FP (2008) Defining genetic interaction. Proc Natl Acad Sci U S A 105: 3461-3466.
43. 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.
44. Jasnos L, Korona R (2007) Epistatic buffering of fitness loss in yeast double deletion strains. Nat Genet 39: 550-554.
45. Segrè D, Deluna A, Church GM, Kishony R (2005) Modular epistasis in yeast metabolism. Nat Genet 37: 77-83.
46. Järvinen AP, Hiissa J, Elo LL, Aittokallio T (2008) Predicting quantitative genetic interactions by means of sequential matrix approximation. PLoS One 3: e3284.
47. Kahana JA, Schlenstedt G, Evanchuk DM, Geiser JR, Hoyt MA, et al. (1998) The yeast dynactin complex is involved in partitioning the mitotic spindle between mother and daughter cells during anaphase B. Mol Biol Cell 9: 1741-1756.
48. Palmer RE, Sullivan DS, Huffaker T, Koshland D (1992) Role of astral microtubules and actin in spindle orientation and migration in the budding yeast, Saccharomyces cerevisiae. J Cell Biol 119: 583-593.
49. Cleves AE, Novick PJ, Bankaitis VA (1989) Mutations in the SAC1 gene suppress defects in yeast Golgi and yeast actin function. J Cell Biol 109: 2939-2950.
50. Zhai C, Li K, Markaki V, Phelan JP, Bowers K, et al. (2008) Ypp1/YGR198w plays an essential role in phosphoinositide signalling at the plasma membrane. Biochem J 415: 455-466.
51. Thompson DA, Stahl FW (1999) Genetic control of recombination partner preference in yeast meiosis: isolation and characterization of mutants elevated for meiotic unequal sister-chromatid recombination. Genetics 153: 621-641.
52. Wang X, Watt PM, Louis EJ, Borts RH, Hickson ID (1996) Pat1: a topoisomerase II-associated protein required for faithful chromosome transmission in Saccharomyces cerevisiae. Nucleic Acids Res 23: 4791-4797.
53. Smialowski P, Pagel P, Wong P, Brauner B, Dunger, et al. (2010) The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res 38: D540-D544.
54. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 33: D535-D539.
55. Meluh PB, Pan X, Yuan DS, Tiffany C, Chen O, et al. (2008) Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray. Methods Mol Biol 416: 221-47.
56. Costanzo M, Boone C (2009) SGAM: an array-based approach for highresolution genetic mapping in Saccharomyces cerevisiae. Methods Mol Biol 548: 37-53.
57. Golub GH, Van Loan CF (1989) Matrix Computations. Second edition. Baltimore: The Johns Hopkins University Press.
58. De Leeuw J (2006) A Decomposition Method for Weighted Least Squares Lowrank Approximation of Symmetric Matrices. Department of Statistics Papers, Paper 2006041602. Available: http://repositories.cdlib.org/uclastat/papers/2006041602. Accessed: June 2010.
59. Liu L, Hawkins DM, Ghosh S, Young SS (2003) Robust singular value decomposition analysis of microarray data. Proc Natl Acad Sci U S A 100: 13167-13172.
60. Tukey JW (1977) Exploratory Data Analysis. Reading Massachusetts: Addison-Wesley.
61. Fawcett T (2004) ROC Graphs: Notes and Practical Considerations for Researchers. HP Laboratories. Available: http://home.comcast.net/,tom.fawcett/public_html/papers/ROC101.pdf. Accessed: June 2010.
62. Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP (2004) A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 20: 323-331.