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iPTMnet: Integrative Bioinformatics for Studying PTM Networks

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Protein Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1558))

Abstract

Protein post-translational modification (PTM) is an essential cellular regulatory mechanism, and disruptions in PTM have been implicated in disease. PTMs are an active area of study in many fields, leading to a wealth of PTM information in the scientific literature. There is a need for user-friendly bioinformatics resources that capture PTM information from the literature and support analyses of PTMs and their functional consequences. This chapter describes the use of iPTMnet (http://proteininformationresource.org/iPTMnet/), a resource that integrates PTM information from text mining, curated databases, and ontologies and provides visualization tools for exploring PTM networks, PTM crosstalk, and PTM conservation across species. We present several PTM-related queries and demonstrate how they can be addressed using iPTMnet.

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Acknowledgments

This work was funded by grants from the National Institutes of Health (U01GM120953 and P20GM103446).

Author information

Authors and Affiliations

  1. Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC, 20057, USA

    Cathy H. Wu

  2. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA

    Hongzhan Huang, Jia Ren, Cecilia N. Arighi, Catalina O. Tudor, Mengxi Lv, Sheng-Chih Chen & Cathy H. Wu

  3. Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA

    Cecilia N. Arighi, Gang Li, K. Vijay-Shanker & Cathy H. Wu

  4. Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19711, USA

    Jung-Youn Lee

  5. Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven Street NW, Suite 1200, Washington, DC, 20057, USA

    Karen E. Ross

Authors
  1. Karen E. Ross
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  2. Hongzhan Huang
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  3. Jia Ren
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  4. Cecilia N. Arighi
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  5. Gang Li
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  6. Catalina O. Tudor
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  7. Mengxi Lv
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  8. Jung-Youn Lee
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  9. Sheng-Chih Chen
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  10. K. Vijay-Shanker
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  11. Cathy H. Wu
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Corresponding author

Correspondence to Karen E. Ross .

Editor information

Editors and Affiliations

  1. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA

    Cathy H. Wu

  2. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA

    Cecilia N. Arighi

  3. Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia, USA

    Karen E. Ross

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Ross, K.E. et al. (2017). iPTMnet: Integrative Bioinformatics for Studying PTM Networks. In: Wu, C., Arighi, C., Ross, K. (eds) Protein Bioinformatics. Methods in Molecular Biology, vol 1558. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6783-4_16

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  • DOI: https://doi.org/10.1007/978-1-4939-6783-4_16

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6781-0

  • Online ISBN: 978-1-4939-6783-4

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