Mining for genotype-phenotype relations in Saccharomyces using partial least squares

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Mehmood, Tahir ^a   Martens, Harald ^a   Sæbø, Solve ^a   Warringer, Jonas ^a,b   Snipen, Lars ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR RESPIRATION; COPY NUMBER VARIATIONS; EXTRACTING INFORMATION; GENOME-WIDE ASSOCIATION STUDIES; MULTIVARIATE APPROACH; PARTIAL LEAST SQUARE (PLS); PHENOTYPIC VARIATIONS; YEAST SACCHAROMYCES CEREVISIAE;

BIOLOGY; LEAST SQUARES APPROXIMATIONS; YEAST;

GENES;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; GENETICS; GENOMICS; GENOTYPE; MOLECULAR EVOLUTION; PHENOTYPE; PHYLOGENY; REGRESSION ANALYSIS; SACCHAROMYCES CEREVISIAE;

EVOLUTION, MOLECULAR; GENOMICS; GENOTYPE; LEAST-SQUARES ANALYSIS; PHENOTYPE; PHYLOGENY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 79960985399     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-318     Document Type: Article

References (61)

1. O'Connor TD, Mundy NI. Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate. Bioinformatics 2009, 25(12):i94-100. 10.1093/bioinformatics/btp231, 2687985, 19478022.
2. Tamura M, D'haeseleer P. Microbial genotype-phenotype mapping by class association rule mining. Bioinformatics 2008, 24:1523-1529. 10.1093/bioinformatics/btn210, 2718668, 18467347.
3. Perlstein EO, Ruderfer DM, Roberts DC, Schreiber SL, Kruglyak L. Genetic basis of individual differences in the response to small-molecule drugs in yeast. Nature Genetics 2007, 39(4):496-502. 10.1038/ng1991, 17334364.
4. Zeyl C. Budding yeast as a model organism for population genetics. Yeast 2000, 16:773-784. 10.1002/1097-0061(20000615)16:8<773::AID-YEA599>3.0.CO;2-1, 10861902.
5. Brauer MJ, Christianson CM, Pai DA, Dunham MJ. Mapping novel traits by array-assisted bulk segregant analysis in Saccharomyces cerevisiae. Genetics 2006, 173:1813-1816. 10.1534/genetics.106.057927, 1526703, 16624899.
6. Berger AC, Vanderford TH, Gernert KM, Nichols JW, Faundez V, Corbett1 AH. Saccharomyces cerevisiae Npc2p is a functionally conserved homologue of the human Niemann-Pick disease type C 2 protein, hNPC2. Eukaryotic Cell 2005, 4:1851-1862. 10.1128/EC.4.11.1851-1862.2005, 1287848, 16278452.
7. Lehner B. Modelling genotype-phenotype relationships and human disease with genetic interaction networks. Journal of Experimental Biology 2007, 210(Pt 9):1559-66.
8. Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, Onge RPS, Tyers M, Koller D, Altman RB, Davis RW, Nislow C, Giaever G. The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 2008, 320(5874):362-5. 10.1126/science.1150021, 2794835, 18420932.
9. Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJT, van Oudenaarden A, Barton DBH, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ. Population genomics of domestic and wild yeasts. Nature 2009, 458:337-341. 10.1038/nature07743, 2659681, 19212322.
10. Badano A. Modeling the bidirectional reflectance of emissive displays. Appl Opt 2002, 41:3847-3852. 10.1364/AO.41.003847, 12099591.
11. Allison DB, Thiel B, Jean PS, Elston RC, Infante MC, Schork NJ. Multiple phenotype modeling in genemapping studies of quantitative traits: power ad-vantages. Am J Hum Genet 1998, 63:1190-1201. 10.1086/302038, 1377471, 9758596.
12. Kraft P, de Andrade M. Group 6: Pleiotropy and multivariate analysis. Genetic Epidemiology 2003, 25(Suppl 1):S50-56.
13. Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, Jaramillo DF, Chu AM, Jordan MI, Arkin AP, Davis RW. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. The National Academy of Sciences 2004, 101:793-798.
14. Parsons AB, Lopez A, Givoni IE, Williams DE, Gray CA, Porter J, Chua G, Sopko R, Brost RL, Ho CH, Wang J, Ketela T, Brenner C, Brill JA, Fernandez GE, Lorenz TC, Payne GS, Ishihara S, Ohya Y, Andrews B, Hughes TR, Frey BJ, Graham TR, Andersen RJ, Boone C. Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell 2006, 126:611-625. 10.1016/j.cell.2006.06.040, 16901791.
15. Jiang C, Zengt ZB. Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 1995, 140:1111-1127. 1206666, 7672582.
16. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34:166-176. 10.1038/ng1165, 12740579.
17. Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S, Shapiro JA, Gresham D, Caudy AA, Kruglyak L. Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 2010, 464:1039-1042. 10.1038/nature08923, 2862354, 20393561.
18. Sæbø S, Almøy T, Aarøe J, Aastveit AH. ST-PLS: a multi-dimensional nearest shrunken centroid type classifier via PLS. Jornal of Chemometrics 2007, 20:54-62.
19. Cao KAL, Rossouw D, Robert-Granie C, Besse P. A sparse PLS for variable selection when integrating omics data. Statistical Applications in Genetics and Molecular Biology 2008, 7:Article 35.
20. Ma BG. How to describe genes: enlightenment from the quaternary number system. Biosystems 2007, 90:20-7. 10.1016/j.biosystems.2006.06.004, 16945479.
21. Kudenko D, Hirsh H. Feature Generation for Sequence Categorization. In Proceedings of the Fifteenth National Conference on Artificial Intelligence 1998, 733-738.
22. Islamaj R, Getoor L, Wilbur WJ. A feature generation algorithm for sequences with application to splice-site prediction. In Proceedings of European Conference on Principles and Practice of Knowledge Discovery in Databases 2006, 553-560.
23. Kruglyak L. The road to genome-wide association studies. Nat Rev Genet 2008, 9:314-318.
24. Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nature Genetics 1999, 21:108-110. 10.1038/5052, 9916801.
25. Snel B, Huynen MA, Dutilh BE. Genome trees and the nature of genome evolution. Annual Review of Microbiology 2005, 59:191-209. 10.1146/annurev.micro.59.030804.121233, 16153168.
26. Gutkin M, Shamir R, Dror G. SlimPLS: a method for feature selection in gene expression-based disease classification. PLoS One 2009, 4(7):e6416. 10.1371/journal.pone.0006416, 2715895, 19649265.
27. Martens H, Næs T. Multivariate Calibration 1989, Wiley.
28. Nguyen DV, Rocke DM. Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 2002, 18:39-50. 10.1093/bioinformatics/18.1.39, 11836210.
29. Nguyen DV, Rocke DM. Multi-class classification via partial least squares with gene expression profiles. Bioinformatics 2002, 18(9):1216-1226. 10.1093/bioinformatics/18.9.1216, 12217913.
30. Aarøe J, Lindahl T, Dumeaux V, Sæbø S, Tobin D, Hagen N, Skaane P, Lønneborg A, Sharma P, Børresen-Dal AL. Gene expression profiling of peripheral blood cells for early detection of breast cancer. Breast Cancer Research 2010, 12.
31. Martens H, Martens M. Multivariate Analysis of Quality-An Introduction 2001, Wiley.
32. Tibshirani R, Hastie T, Narasimhan B, Chu G. Class Prediction by Nearest Shrunken Centroids, with Applications to DNA Microarrays. Statisitcal Science 2003, 18:104-117.
33. Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maierl A, Oliver SG, Pfei er F, Zollner A. Overview of the yeast genome. Nature 1997, 387:7-65.
34. Liti G, Louis EJ. Yeast evolution and comparative genomics. Annual Review of Microbiology 2005, 59:135-153. 10.1146/annurev.micro.59.030804.121400, 15877535.
35. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254. 10.1038/nature01644, 12748633.
36. Warringer J, Zorgo E, Cubillos FA, Gjuvsland A, Louis EJ, Omholt S, Liti G, Moses A, Blomberg A. Trait Variation in Yeast Is Defined by Population History. PLoS Genetics 2011,
37. Warringer J, Anevski D, Liu B, Blomberg A. Chemogenetic fingerprinting by analysis of cellular growth dynamics. BMC Chemical Biology 2008, 8:3. 10.1186/1472-6769-8-3, 2532679, 18721464.
38. Warringer J, Blomberg A. Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cere-visiae. Yeast 2003, 20:53-67. 10.1002/yea.931, 12489126.
39. Indahl U. A twist to partial least squares regression. Jornal of Chemometrics 2005, 19:32-44.
40. Rajalahti T, Arneberg R, Kroksveen AC, Berle M, Myhr KM, Kvalheim OM. Discriminating variable test and selectivity ratio plot: quantitative tools for interpretation and variable (biomarker) selection in complex spectral or chromatographic profiles. Analytical Chemistry 2009, 81(7):2581-90. 10.1021/ac802514y, 19228047.
41. Liland KH, Indahl UG. Powered partial least squares discriminant analysis. Jornal of Chemometrics 2009, 23(1-2):7-18.
42. Dimmer EC, Huntley RP, Barrell DG, Binns D, Draghici S, Camon EB, Hubank M, Talmud PJ, Apweiler R, Lovering RC. The Gene Ontology - Providing a Functional Role in Proteomic Studies. Proteomics 2008,
43. R JTCC. Evolution of Protein Molecules. Mammalian protein metabolism 1969, 3:21-123.
44. Willmott CJ. On the valldatlon of models. Phys Geogr 1981, 2:184-187.
45. Singleton P, Sainsbury D. Dictionary of Microbiology and Molecular Biology 2001, 106. John Wiley and Sons, Chichester, UK.
46. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. Genomic expression programs in the response of yeast cells to en-vironmental changes. Mol Biol Cell 2000, 11:4241-4257. 15070, 11102521.
47. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 2001, 12:323-337. 30946, 11179418.
48. Wall D, Hirsh A, Fraser H, Kumm J, Giaever G, Eisen M, Feldman M. Functional genomic analysis of the rates of protein evolution. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(15):5483. 10.1073/pnas.0501761102, 555735, 15800036.
49. Hohmann S. Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev 2002, 66:300-372. 10.1128/MMBR.66.2.300-372.2002, 120784, 12040128.
50. Warringer J, Ericson E, Fernandez L, Nerman O, Blomberg A. High-resolution yeast phenomics resolves different physiological features in the saline response. Proc Natl Acad Sci USA 2003, 100:15724-15729. 10.1073/pnas.2435976100, 307635, 14676322.
51. Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, Davis RW. Dissecting the architecture of a quantitative trait locus in yeast. Nature 2002, 416:326-330. 10.1038/416326a, 11907579.
52. Ruiz-Roig C, Vieitez C, Posas F, de Nadal E. The Rpd3L HDAC complex is essential for the heat stress response in yeast. Mol Microbiol 2010, 76:1049-1062. 10.1111/j.1365-2958.2010.07167.x, 20398213.
53. Scharfe C, Lu HH, Neuenburg JK, Allen EA, Li GC, Klopstock T, Cowan TM, Enns GM, Davis RW. Map-ping gene associations in human mitochondria using clinical disease phenotypes. PLoS Comput Biol 2009, 5:e1000374. 10.1371/journal.pcbi.1000374, 2668170, 19390613.
54. Dujon B. Yeast evolutionary genomics. Nat Rev Genet 2010, 11:512-524.
55. Gaisne M, Becam AM, Verdiere J, Herbert CJ. A 'natural' mutation in Saccharomyces cerevisiae strains derived from S288c affects the complex regulatory gene HAP1 (CYP1). Curr Genet 1999, 36:195-200. 10.1007/s002940050490, 10541856.
56. Springer NM, Stupar RM. Allelic variation and heterosis in maize: how do two halves make more than a whole?. Genome Res 2007, 17:264-275. 10.1101/gr.5347007, 17255553.
57. Cohen BA, Mitra RD, Hughes JD, Church GM. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 2000, 26:183-186. 10.1038/79896, 11017073.
58. Dudley AM, Janse DM, Tanay A, Shamir R, Church GM. A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol 2005, 1. 2005.0001.
59. Ericson E, Pylvanainen I, Fernandez-Ricaud L, Nerman O, Warringer J, Blomberg A. Genetic pleiotropy in Saccharomyces cerevisiae quantified by high-resolution phenotypic profiling. Mol Genet Genomics 2006, 275:605-614. 10.1007/s00438-006-0112-1, 16534619.
60. Pal C, Hurst LD. evidence for co-evolution of gene order and recombination rate. Nat Genet 2003, 33:392-395. 10.1038/ng1111, 12577060.
61. Will JL, Kim HS, Clarke J, Painter JC, Fay JC, Gasch AP. Incipient balancing selection through adaptive loss of aquaporins in natural Saccha-romyces cerevisiae populations. PLoS Genet 2010, 6:e1000893. 10.1371/journal.pgen.1000893, 2848549, 20369021.