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Research Article

High-dimensional and large-scale phenotyping of yeast mutants

Yoshikazu Ohya, Jun Sese, Masashi Yukawa, Fumi Sano, Yoichiro Nakatani, Taro L. Saito, Ayaka Saka, Tomoyuki Fukuda, Satoru Ishihara, Satomi Oka, Genjiro Suzuki, Machika Watanabe, Aiko Hirata, Miwaka Ohtani, Hiroshi Sawai, Nicolas Fraysse, Jean-Paul Latgé, Jean M. François, Markus Aebi, Seiji Tanaka, Sachiko Muramatsu, Hiroyuki Araki, Kintake Sonoike, Satoru Nogami, and Shinichi Morishita
  1. Departments of *Integrated Biosciences and §Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; †Institute for Bioinformatics and Research and Development, Japan Science and Technology Corporation, Science Plaza 5-3 Yonbancho, Chiyoda-ku, Tokyo 102-8666, Japan; ∥Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; **Unité des Aspergillus, Institut Pasteur, 25 Rue du Docteur Roux, 75015 Paris, France; ††Centre de Bioingenierie Gilbert Durand, Unité Mixte de Recherche-Centre National de la Recherche Scientifique 5504, Unité Mixte de Recherche-Institut National de la Recherche Agronomique 792, F31077 Toulouse Cedex, France; ‡‡Institute of Microbiology, Swiss Federal Institute of Technology, Eidgenössiche Technische Hochschule-Honggerberg, CH-8093 Zurich, Switzerland; and §§Division of Microbial Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan

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PNAS December 27, 2005 102 (52) 19015-19020; https://doi.org/10.1073/pnas.0509436102
Yoshikazu Ohya
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Jun Sese
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Masashi Yukawa
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Fumi Sano
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Yoichiro Nakatani
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Taro L. Saito
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Ayaka Saka
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Tomoyuki Fukuda
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Satoru Ishihara
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Satomi Oka
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Genjiro Suzuki
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Machika Watanabe
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Aiko Hirata
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Miwaka Ohtani
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Hiroshi Sawai
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Nicolas Fraysse
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Jean-Paul Latgé
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Jean M. François
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Markus Aebi
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Seiji Tanaka
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Sachiko Muramatsu
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Hiroyuki Araki
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Kintake Sonoike
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Satoru Nogami
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Shinichi Morishita
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  1. Communicated by David Botstein, Princeton University, Princeton, NJ, October 31, 2005 (received for review August 8, 2005)

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Abstract

One of the most powerful techniques for attributing functions to genes in uni- and multicellular organisms is comprehensive analysis of mutant traits. In this study, systematic and quantitative analyses of mutant traits are achieved in the budding yeast Saccharomyces cerevisiae by investigating morphological phenotypes. Analysis of fluorescent microscopic images of triple-stained cells makes it possible to treat morphological variations as quantitative traits. Deletion of nearly half of the yeast genes not essential for growth affects these morphological traits. Similar morphological phenotypes are caused by deletions of functionally related genes, enabling a functional assignment of a locus to a specific cellular pathway. The high-dimensional phenotypic analysis of defined yeast mutant strains provides another step toward attributing gene function to all of the genes in the yeast genome.

  • cell morphology
  • functional genomics
  • high-dimensional phenotyping
  • phenome

Footnotes

  • ↵ ‡ To whom correspondence may be addressed. E-mail. ohya{at}k.u-tokyo.ac.jp or (for bioinformatics questions) moris{at}cb.k.u-tokyo.ac.jp.

  • ↵ ¶ J.S. and M.Y. contributed equally to this work.

  • Author contributions: Y.O. and S. Morishita designed research; M.Y., F.S., A.S., T.F., S.I., S.O., G.S., M.W., A.H., N.F., S.T., S. Muramatsu, and S.N. performed research; J.-P.L., J.M.F., M.A., H.A., and K.S. contributed new reagents/analytic tools; J.S., Y.N., M.O., and H.S. analyzed data; Y.O. and S.N. wrote the paper; J.S. predicted relationship between morphology and gene function; M.Y. designed experiments and performed biological analysis; F.S. collected morphological data of mutants; Y.N. estimated morphological mutants; and T.L.S. constructed and managed database web site.

  • Conflict of interest statement: No conflicts declared.

  • Abbreviation: GO, gene ontology.

  • Freely available online through the PNAS open access option.

  • Copyright © 2005, The National Academy of Sciences
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High-dimensional and large-scale phenotyping of yeast mutants
Yoshikazu Ohya, Jun Sese, Masashi Yukawa, Fumi Sano, Yoichiro Nakatani, Taro L. Saito, Ayaka Saka, Tomoyuki Fukuda, Satoru Ishihara, Satomi Oka, Genjiro Suzuki, Machika Watanabe, Aiko Hirata, Miwaka Ohtani, Hiroshi Sawai, Nicolas Fraysse, Jean-Paul Latgé, Jean M. François, Markus Aebi, Seiji Tanaka, Sachiko Muramatsu, Hiroyuki Araki, Kintake Sonoike, Satoru Nogami, Shinichi Morishita
Proceedings of the National Academy of Sciences Dec 2005, 102 (52) 19015-19020; DOI: 10.1073/pnas.0509436102

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High-dimensional and large-scale phenotyping of yeast mutants
Yoshikazu Ohya, Jun Sese, Masashi Yukawa, Fumi Sano, Yoichiro Nakatani, Taro L. Saito, Ayaka Saka, Tomoyuki Fukuda, Satoru Ishihara, Satomi Oka, Genjiro Suzuki, Machika Watanabe, Aiko Hirata, Miwaka Ohtani, Hiroshi Sawai, Nicolas Fraysse, Jean-Paul Latgé, Jean M. François, Markus Aebi, Seiji Tanaka, Sachiko Muramatsu, Hiroyuki Araki, Kintake Sonoike, Satoru Nogami, Shinichi Morishita
Proceedings of the National Academy of Sciences Dec 2005, 102 (52) 19015-19020; DOI: 10.1073/pnas.0509436102
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