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Uniform Curation Protocol of Metazoan Signaling Pathways to Predict Novel Signaling Components

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In Silico Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1021))

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Abstract

A relatively large number of signaling databases available today have strongly contributed to our understanding of signaling pathway properties. However, pathway comparisons both within and across databases are currently severely hampered by the large variety of data sources and the different levels of detail of their information content (on proteins and interactions). In this chapter, we present a protocol for a uniform curation method of signaling pathways, which intends to overcome this insufficiency. This uniformly curated database called SignaLink (http://signalink.org) allows us to systematically transfer pathway annotations between different species, based on orthology, and thereby to predict novel signaling pathway components. Thus, this method enables the compilation of a comprehensive signaling map of a given species and identification of new potential drug targets in humans.

We strongly believe that the strict curation protocol we have established to compile a signaling pathway database can also be applied for the compilation of other (e.g., metabolic) databases. Similarly, the detailed guide to the orthology-based prediction of novel signaling components across species may also be utilized for predicting components of other biological processes.

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Acknowledgement

Authors were supported by the European Union and the European Social Fund [TAMOP-4.2.1/B-09/1/KMR-2010-0003], the Hungarian Scientific Research Fund [OTKA K75334, NK78012], and a János Bolyai Scholarship to TK and TV.

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Authors and Affiliations

  1. Department of Genetics, Eötvös Loránd University, Budapest, Hungary

    Máté Pálfy, Tibor Vellai & Tamás Korcsmáros

  2. Statistical and Biological Physics Group of the Hungarian Academy of Sciences, Budapest, Hungary

    Illés J. Farkas

Authors
  1. Máté Pálfy
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  2. Illés J. Farkas
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  3. Tibor Vellai
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  4. Tamás Korcsmáros
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Editor information

Editors and Affiliations

  1. The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom

    Maria Victoria Schneider

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Pálfy, M., Farkas, I.J., Vellai, T., Korcsmáros, T. (2013). Uniform Curation Protocol of Metazoan Signaling Pathways to Predict Novel Signaling Components. In: Schneider, M. (eds) In Silico Systems Biology. Methods in Molecular Biology, vol 1021. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-450-0_15

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  • DOI: https://doi.org/10.1007/978-1-62703-450-0_15

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-449-4

  • Online ISBN: 978-1-62703-450-0

  • eBook Packages: Springer Protocols

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