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Biological Networks and Pathway Analysis pp 311–331Cite as

Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1613))

Abstract

It is becoming more evident that computational methods are needed for the identification and the mapping of pathways in new genomes. We introduce an automatic annotation system (ARBA4Path Association Rule-Based Annotator for Pathways) that utilizes rule mining techniques to predict metabolic pathways across wide range of prokaryotes. It was demonstrated that specific combinations of protein domains (recorded in our rules) strongly determine pathways in which proteins are involved and thus provide information that let us very accurately assign pathway membership (with precision of 0.999 and recall of 0.966) to proteins of a given prokaryotic taxon. Our system can be used to enhance the quality of automatically generated annotations as well as annotating proteins with unknown function. The prediction models are represented in the form of human-readable rules, and they can be used effectively to add absent pathway information to many proteins in UniProtKB/TrEMBL database.

*These authors contributed equally to this work.

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Acknowledgments

The second author conducted this work as part of a research internship at the European Bioinformatics Institute, UniProt team. The funding for this internship was provided by King Abdullah University of Science and Technology. The authors would also like to thank UniProt Consortium for their valuable support and feedback on the development of this work.

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    Authors and Affiliations

    1. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK

      Rabie Saidi

    2. Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Kingdom of Saudi Arabia

      Imane Boudellioua & Maria J. Martin

    3. Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY, 10549, USA

      Victor Solovyev

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    1. Rabie Saidi
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    2. Imane Boudellioua
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    4. Victor Solovyev
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    Correspondence to Rabie Saidi or Victor Solovyev .

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    Editors and Affiliations

    1. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

      Tatiana V. Tatarinova

    2. Prosapia Genetics, Solana Beach, California, USA

      Yuri Nikolsky

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    Saidi, R., Boudellioua, I., Martin, M.J., Solovyev, V. (2017). Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways. In: Tatarinova, T., Nikolsky, Y. (eds) Biological Networks and Pathway Analysis. Methods in Molecular Biology, vol 1613. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7027-8_12

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    • DOI: https://doi.org/10.1007/978-1-4939-7027-8_12

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