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Integrated network analysis platform for protein-protein interactions

Nature Methods volume 6, pages 75–77 (2009)Cite this article

Abstract

There is an increasing demand for network analysis of protein-protein interactions (PPIs). We introduce a web-based protein interaction network analysis platform (PINA), which integrates PPI data from six databases and provides network construction, filtering, analysis and visualization tools. We demonstrated the advantages of PINA by analyzing two human PPI networks; our results suggested a link between LKB1 and TGFβ signaling, and revealed possible competitive interactors of p53 and c-Jun.

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Figure 1: Schematic of the PINA platform.
Figure 2: PINA-generated visualization of the PPI networks for LKB1 and its 14 substrate kinases.

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Acknowledgements

This work was supported by the European Union Sixth Framework Programme grant European Network for Functional Integration (LSHG-CT-2005-518254), Sigrid Jusélius Foundation, University of Helsinki's Research Funds, Academy of Finland (projects 125826, 213345 and 1121413), Finnish Cancer Association, Emil Aaltonen Foundation and competitive research funding of the Pirkanmaa Hospital District.

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Author notes

  1. Tea Vallenius and Kristian Ovaska: These authors contributed equally to this work.

Authors and Affiliations

  1. Genome-Scale Biology Program, Institute of Biomedicine, University of Helsinki, Haartmaninkatu 8, Helsinki, 00014, Finland

    Jianmin Wu, Tea Vallenius, Kristian Ovaska, Tomi P Mäkelä & Sampsa Hautaniemi

  2. Institute of Medical Technology, University of Tampere and Tampere University Hospital, Biokatu 8, Tampere, 33520, Finland

    Jukka Westermarck

  3. Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6A, Turku, 23520, Finland

    Jukka Westermarck

Authors
  1. Jianmin Wu
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  2. Tea Vallenius
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  3. Kristian Ovaska
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  4. Jukka Westermarck
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  5. Tomi P Mäkelä
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  6. Sampsa Hautaniemi
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Contributions

Ji.W. designed and implemented the PINA platform; T.V. and T.P.M. designed the LKB1 case study and recurated corresponding interactions; K.O. implemented graph and GO tools; Ju.W. designed the p53–c-Jun case study and recurated corresponding interactions; T.P.M initiated the project; S.H. did overall design and supervised the project. All authors participated in manuscript writing.

Corresponding author

Correspondence to Jianmin Wu.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3, Supplementary Methods (PDF 2861 kb)

Supplementary Table 1

Classification of discarded interactions in the two case studies. (XLS 53 kb)

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Wu, J., Vallenius, T., Ovaska, K. et al. Integrated network analysis platform for protein-protein interactions. Nat Methods 6, 75–77 (2009). https://doi.org/10.1038/nmeth.1282

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