ProSNet: Integrating homology with molecular networks for protein function prediction

Sheng Wang, Meng Qu, Jian Peng

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Automated annotation of protein function has become a critical task in the post-genomic era. Network-based approaches and homology-based approaches have been widely used and recently tested in large-scale community-wide assessment experiments. It is natural to integrate network data with homology information to further improve the predictive performance. However, integrating these two heterogeneous, high-dimensional and noisy datasets is non-trivial. In this work, we introduce a novel protein function prediction algorithm ProSNet. An integrated heterogeneous network is first built to include molecular networks of multiple species and link together homologous proteins across multiple species. Based on this integrated network, a dimensionality reduction algorithm is introduced to obtain compact low-dimensional vectors to encode proteins in the network. Finally, we develop machine learning classification algorithms that take the vectors as input and make predictions by transferring annotations both within each species and across different species. Extensive experiments on five major species demonstrate that our integration of homology with molecular networks substantially improves the predictive performance over existing approaches.

Original languageEnglish (US)
Title of host publicationPACIFIC SYMPOSIUM ON BIOCOMPUTING 2017
EditorsRuss B. Altman, Tiffany Murray, Teri E. Klein, A. Keith Dunker, Marylyn D. Ritchie, Lawrence Hunter
PublisherWorld Scientific Publishing Co. Pte Ltd
Pages27-38
Number of pages12
Edition212679
ISBN (Print)9789813207813
DOIs
StatePublished - Jan 1 2017
Event22nd Pacific Symposium on Biocomputing, PSB 2017 - Kohala Coast, United States
Duration: Jan 4 2017Jan 8 2017

Publication series

NamePacific Symposium on Biocomputing, 2017
Number212679

Other

Other22nd Pacific Symposium on Biocomputing, PSB 2017
CountryUnited States
CityKohala Coast
Period1/4/171/8/17

Keywords

  • Data integration
  • Dimensionality reduction
  • Homology
  • Molecular networks
  • Protein function prediction

ASJC Scopus subject areas

  • Biomedical Engineering
  • Computational Theory and Mathematics
  • Medicine(all)

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  • Cite this

    Wang, S., Qu, M., & Peng, J. (2017). ProSNet: Integrating homology with molecular networks for protein function prediction. In R. B. Altman, T. Murray, T. E. Klein, A. K. Dunker, M. D. Ritchie, & L. Hunter (Eds.), PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017 (212679 ed., pp. 27-38). (Pacific Symposium on Biocomputing, 2017; No. 212679). World Scientific Publishing Co. Pte Ltd. https://doi.org/10.1142/9789813207813_0004