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Global analysis of protein phosphorylation in yeast

Author

Listed:
  • Jason Ptacek

    (Department of Molecular Biophysics and Biochemistry)

  • Geeta Devgan

    (Yale University)

  • Gregory Michaud

    (Invitrogen Corporation)

  • Heng Zhu

    (Yale University)

  • Xiaowei Zhu

    (Yale University)

  • Joseph Fasolo

    (Yale University)

  • Hong Guo

    (Invitrogen Corporation)

  • Ghil Jona

    (Yale University)

  • Ashton Breitkreutz

    (University of Toronto, 1 King's College Circle)

  • Richelle Sopko

    (University of Toronto, 1 King's College Circle)

  • Rhonda R. McCartney

    (University of Pittsburgh School of Medicine)

  • Martin C. Schmidt

    (University of Pittsburgh School of Medicine)

  • Najma Rachidi

    (School of Life Sciences, University of Dundee)

  • Soo-Jung Lee

    (Yale University School of Medicine)

  • Angie S. Mah

    (California Institute of Technology)

  • Lihao Meng

    (Invitrogen Corporation)

  • Michael J. R. Stark

    (School of Life Sciences, University of Dundee)

  • David F. Stern

    (Yale University School of Medicine)

  • Claudio De Virgilio

    (University of Geneva)

  • Mike Tyers

    (University of Toronto, 1 King's College Circle)

  • Brenda Andrews

    (University of Toronto, 1 King's College Circle
    University of Toronto, Room 4285, Medical Sciences Building, 1 King's College Circle
    University of Toronto, Room 4285, Medical Sciences Building, 1 King's College Circle)

  • Mark Gerstein

    (Department of Molecular Biophysics and Biochemistry)

  • Barry Schweitzer

    (Invitrogen Corporation)

  • Paul F. Predki

    (Invitrogen Corporation)

  • Michael Snyder

    (Department of Molecular Biophysics and Biochemistry
    Yale University)

Abstract

Kinases on the map Protein phosphorylation is involved in the regulation of many basic cellular processes, so it is a prime target for analysis by proteomics. Proteome chip technology has now been used to produce a first-generation map of the global phosphorylation networks in yeast. More than 4,000 interactions were found for over 1,300 proteins, and substrates were identified for the majority of yeast kinases. Many of the yeast proteins and pathways are conserved in other eukaryotes, so this new resource will be of relevance to the mechanisms of protein phosphorylation in many other organisms. All of the data are freely available in a searchable format.

Suggested Citation

  • Jason Ptacek & Geeta Devgan & Gregory Michaud & Heng Zhu & Xiaowei Zhu & Joseph Fasolo & Hong Guo & Ghil Jona & Ashton Breitkreutz & Richelle Sopko & Rhonda R. McCartney & Martin C. Schmidt & Najma Ra, 2005. "Global analysis of protein phosphorylation in yeast," Nature, Nature, vol. 438(7068), pages 679-684, December.
    • Handle: RePEc:nat:nature:v:438:y:2005:i:7068:d:10.1038_nature04187
    DOI: 10.1038/nature04187
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    Citations

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    Cited by:

    1. Saket Navlakha & Anthony Gitter & Ziv Bar-Joseph, 2012. "A Network-based Approach for Predicting Missing Pathway Interactions," PLOS Computational Biology, Public Library of Science, vol. 8(8), pages 1-13, August.
    2. Jacob D Feala & Jorge Cortes & Phillip M Duxbury & Andrew D McCulloch & Carlo Piermarocchi & Giovanni Paternostro, 2012. "Statistical Properties and Robustness of Biological Controller-Target Networks," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-11, January.
    3. Sourav Bandyopadhyay & Ryan Kelley & Nevan J Krogan & Trey Ideker, 2008. "Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data," PLOS Computational Biology, Public Library of Science, vol. 4(4), pages 1-8, April.
    4. Pengyi Yang & Xiaofeng Zheng & Vivek Jayaswal & Guang Hu & Jean Yee Hwa Yang & Raja Jothi, 2015. "Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data," PLOS Computational Biology, Public Library of Science, vol. 11(8), pages 1-18, August.
    5. Shinsuke Ohnuki & Yoshikazu Ohya, 2018. "High-dimensional single-cell phenotyping reveals extensive haploinsufficiency," PLOS Biology, Public Library of Science, vol. 16(5), pages 1-23, May.
    6. Thomas C Whisenant & David T Ho & Ryan W Benz & Jeffrey S Rogers & Robyn M Kaake & Elizabeth A Gordon & Lan Huang & Pierre Baldi & Lee Bardwell, 2010. "Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors," PLOS Computational Biology, Public Library of Science, vol. 6(8), pages 1-21, August.
    7. Doron Betel & Kevin E Breitkreuz & Ruth Isserlin & Danielle Dewar-Darch & Mike Tyers & Christopher W V Hogue, 2007. "Structure-Templated Predictions of Novel Protein Interactions from Sequence Information," PLOS Computational Biology, Public Library of Science, vol. 3(9), pages 1-7, September.
    8. Silvia Martini & Khalil Davis & Rupert Faraway & Lisa Elze & Nicola Lockwood & Andrew Jones & Xiao Xie & Neil Q. McDonald & David J. Mann & Alan Armstrong & Jernej Ule & Peter J. Parker, 2021. "A genetically-encoded crosslinker screen identifies SERBP1 as a PKCĪµ substrate influencing translation and cell division," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    9. Qi Yu & Xuanyunjing Gong & Yue Tong & Min Wang & Kai Duan & Xinyu Zhang & Feng Ge & Xilan Yu & Shanshan Li, 2022. "Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy," Nature Communications, Nature, vol. 13(1), pages 1-19, December.

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