Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

Bernd Bodenmiller; Stefanie Wanka; Claudine Kraft; Jörg Urban; David Campbell; Patrick G. Pedrioli; Bertran Gerrits; Paola Picotti; Henry Lam; Olga Vitek; Mi-Youn Brusniak; Bernd Roschitzki; Chao Zhang; Kevan M. Shokat; Ralph Schlapbach; Alejandro Colman-Lerner; Garry P. Nolan; Alexey I. Nesvizhskii; Matthias Peter; Robbie Loewith; Christian von Mering; Ruedi Aebersold

doi:10.1126/scisignal.2001182

Research ResourceSystems Biology

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

Bernd Bodenmiller¹,²,*,†,
Stefanie Wanka²,³,*,
Claudine Kraft⁴,
Jörg Urban⁵,
David Campbell⁶,
Patrick G. Pedrioli⁴,‡,
Bertran Gerrits⁷,§,
Paola Picotti¹,
Henry Lam⁸,
Olga Vitek⁹,
Mi-Youn Brusniak⁶,
Bernd Roschitzki⁷,
Chao Zhang¹⁰,
Kevan M. Shokat¹⁰,
Ralph Schlapbach⁷,
Alejandro Colman-Lerner¹¹,
Garry P. Nolan¹²,
Alexey I. Nesvizhskii¹³,
Matthias Peter⁴,
Robbie Loewith⁵,
Christian von Mering³, and
Ruedi Aebersold¹,⁶,¹⁴,||

¹Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
²Zurich PhD Program in Molecular Life Sciences, 8057 Zurich, Switzerland.
³Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.
⁴Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland.
⁵Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland.
⁶Institute for Systems Biology, Seattle, WA 98103, USA.
⁷Functional Genomics Center Zurich, University Zurich and ETH Zurich, 8057 Zurich, Switzerland.
⁸Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
⁹Departments of Statistics and Computer Science, Purdue University, West Lafayette, IN 47107, USA.
¹⁰Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158–2280, USA.
¹¹Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, C1428EHA Buenos Aires, Argentina.
¹²Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
¹³Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
¹⁴Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.

↵||To whom correspondence should be addressed. E-mail: aebersold{at}imsb.biol.ethz.ch

↵* These authors contributed equally to this work.
↵† Present address: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
↵‡ Present address: Scottish Institute for Cell Signalling, Sir James Black Centre, University of Dundee, Dundee, Scotland DD1 5EH, UK.
↵§ Present address: Novartis Institute for Biomedical Research, Novartis International AG, CH-4002 Basel, Switzerland.

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Science Signaling 21 Dec 2010:
Vol. 3, Issue 153, pp. rs4
DOI: 10.1126/scisignal.2001182

Bernd Bodenmiller

1Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.

2Zurich PhD Program in Molecular Life Sciences, 8057 Zurich, Switzerland.

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Stefanie Wanka

2Zurich PhD Program in Molecular Life Sciences, 8057 Zurich, Switzerland.

3Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.

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Claudine Kraft

4Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland.

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Jörg Urban

5Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland.

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David Campbell

6Institute for Systems Biology, Seattle, WA 98103, USA.

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Patrick G. Pedrioli

4Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland.

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Bertran Gerrits

7Functional Genomics Center Zurich, University Zurich and ETH Zurich, 8057 Zurich, Switzerland.

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Paola Picotti

1Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.

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Henry Lam

8Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.

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Olga Vitek

9Departments of Statistics and Computer Science, Purdue University, West Lafayette, IN 47107, USA.

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Mi-Youn Brusniak

6Institute for Systems Biology, Seattle, WA 98103, USA.

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Bernd Roschitzki

7Functional Genomics Center Zurich, University Zurich and ETH Zurich, 8057 Zurich, Switzerland.

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Chao Zhang

10Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158–2280, USA.

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Kevan M. Shokat

10Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158–2280, USA.

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Ralph Schlapbach

7Functional Genomics Center Zurich, University Zurich and ETH Zurich, 8057 Zurich, Switzerland.

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Alejandro Colman-Lerner

11Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, C1428EHA Buenos Aires, Argentina.

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Garry P. Nolan

12Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.

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Alexey I. Nesvizhskii

13Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.

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Matthias Peter

4Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland.

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Robbie Loewith

5Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland.

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Christian von Mering

3Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.

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Ruedi Aebersold

1Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.

6Institute for Systems Biology, Seattle, WA 98103, USA.

14Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.

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For correspondence: aebersold@imsb.biol.ethz.ch

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Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

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