Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

Daniel A. Skelly; Gennifer E. Merrihew; Michael Riffle; Caitlin F. Connelly; Emily O. Kerr; Marnie Johansson; Daniel Jaschob; Beth Graczyk; Nicholas J. Shulman; Jon Wakefield; Sara J. Cooper; Stanley Fields; William S. Noble; Eric G.D. Müller; Trisha N. Davis; Maitreya J. Dunham; Michael J. MacCoss; Joshua M. Akey

doi:10.1101/gr.155762.113

Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

Daniel A. Skelly, Gennifer E. Merrihew, Michael Riffle, Caitlin F. Connelly, Emily O. Kerr, Marnie Johansson, Daniel Jaschob, Beth Graczyk, Nicholas J. Shulman, Jon Wakefield, Sara J. Cooper, Stanley Fields, William S. Noble, Eric G.D. Müller, Trisha N. Davis, Maitreya J. Dunham, Michael J. MacCoss, Joshua M. Akey

Research output: Contribution to journal › Article › peer-review

112 Scopus citations

Abstract

To better understand the quantitative characteristics and structure of phenotypic diversity, we measured over 14,000 transcript, protein, metabolite, and morphological traits in 22 genetically diverse strains of Saccharomyces cerevisiae. More than 50% of all measured traits varied significantly across strains [false discovery rate (FDR) = 5%]. The structure of phenotypic correlations is complex, with 85% of all traits significantly correlated with at least one other phenotype (median = 6, maximum = 328). We show how high-dimensional molecular phenomics data sets can be leveraged to accurately predict phenotypic variation between strains, often with greater precision than afforded by DNA sequence information alone. These results provide new insights into the spectrum and structure of phenotypic diversity and the characteristics influencing the ability to accurately predict phenotypes.

Original language	English (US)
Pages (from-to)	1496-1504
Number of pages	9
Journal	Genome Research
Volume	23
Issue number	9
DOIs	https://doi.org/10.1101/gr.155762.113
State	Published - Sep 2013
Externally published	Yes

All Science Journal Classification (ASJC) codes

Genetics(clinical)
Genetics

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Skelly, D. A., Merrihew, G. E., Riffle, M., Connelly, C. F., Kerr, E. O., Johansson, M., Jaschob, D., Graczyk, B., Shulman, N. J., Wakefield, J., Cooper, S. J., Fields, S., Noble, W. S., Müller, E. G. D., Davis, T. N., Dunham, M. J., MacCoss, M. J., & Akey, J. M. (2013). Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Genome Research, 23(9), 1496-1504. https://doi.org/10.1101/gr.155762.113

@article{8fe3f70671f54c599bc5c726eeea0dae,

title = "Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast",

abstract = "To better understand the quantitative characteristics and structure of phenotypic diversity, we measured over 14,000 transcript, protein, metabolite, and morphological traits in 22 genetically diverse strains of Saccharomyces cerevisiae. More than 50% of all measured traits varied significantly across strains [false discovery rate (FDR) = 5%]. The structure of phenotypic correlations is complex, with 85% of all traits significantly correlated with at least one other phenotype (median = 6, maximum = 328). We show how high-dimensional molecular phenomics data sets can be leveraged to accurately predict phenotypic variation between strains, often with greater precision than afforded by DNA sequence information alone. These results provide new insights into the spectrum and structure of phenotypic diversity and the characteristics influencing the ability to accurately predict phenotypes.",

author = "Skelly, {Daniel A.} and Merrihew, {Gennifer E.} and Michael Riffle and Connelly, {Caitlin F.} and Kerr, {Emily O.} and Marnie Johansson and Daniel Jaschob and Beth Graczyk and Shulman, {Nicholas J.} and Jon Wakefield and Cooper, {Sara J.} and Stanley Fields and Noble, {William S.} and M{\"u}ller, {Eric G.D.} and Davis, {Trisha N.} and Dunham, {Maitreya J.} and MacCoss, {Michael J.} and Akey, {Joshua M.}",

year = "2013",

month = sep,

doi = "10.1101/gr.155762.113",

language = "English (US)",

volume = "23",

pages = "1496--1504",

journal = "Genome Research",

issn = "1088-9051",

publisher = "Cold Spring Harbor Laboratory Press",

number = "9",

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Skelly, DA, Merrihew, GE, Riffle, M, Connelly, CF, Kerr, EO, Johansson, M, Jaschob, D, Graczyk, B, Shulman, NJ, Wakefield, J, Cooper, SJ, Fields, S, Noble, WS, Müller, EGD, Davis, TN, Dunham, MJ, MacCoss, MJ & Akey, JM 2013, 'Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast', Genome Research, vol. 23, no. 9, pp. 1496-1504. https://doi.org/10.1101/gr.155762.113

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T1 - Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

AU - Skelly, Daniel A.

AU - Merrihew, Gennifer E.

AU - Riffle, Michael

AU - Connelly, Caitlin F.

AU - Kerr, Emily O.

AU - Johansson, Marnie

AU - Jaschob, Daniel

AU - Graczyk, Beth

AU - Shulman, Nicholas J.

AU - Wakefield, Jon

AU - Cooper, Sara J.

AU - Fields, Stanley

AU - Noble, William S.

AU - Müller, Eric G.D.

AU - Davis, Trisha N.

AU - Dunham, Maitreya J.

AU - MacCoss, Michael J.

AU - Akey, Joshua M.

PY - 2013/9

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AB - To better understand the quantitative characteristics and structure of phenotypic diversity, we measured over 14,000 transcript, protein, metabolite, and morphological traits in 22 genetically diverse strains of Saccharomyces cerevisiae. More than 50% of all measured traits varied significantly across strains [false discovery rate (FDR) = 5%]. The structure of phenotypic correlations is complex, with 85% of all traits significantly correlated with at least one other phenotype (median = 6, maximum = 328). We show how high-dimensional molecular phenomics data sets can be leveraged to accurately predict phenotypic variation between strains, often with greater precision than afforded by DNA sequence information alone. These results provide new insights into the spectrum and structure of phenotypic diversity and the characteristics influencing the ability to accurately predict phenotypes.

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Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast

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