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Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework

  • Ramanuja Simha
  • Hagit Shatkay
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8126)

Abstract

Knowing the location of a protein within the cell is important for understanding its function, role in biological processes, and potential use as a drug target. Much progress has been made in developing computational methods that predict single locations for proteins, assuming that proteins localize to a single location. However, it has been shown that proteins localize to multiple locations. While a few recent systems have attempted to predict multiple locations of proteins, they typically treat locations as independent or capture inter-dependencies by treating each locations-combination present in the training set as an individual location-class. We present a new method and a preliminary system we have developed that directly incorporates inter-dependencies among locations into the multiple-location-prediction process, using a collection of Bayesian network classifiers. We evaluate our system on a dataset of single- and multi-localized proteins. Our results, obtained by incorporating inter-dependencies are significantly higher than those obtained by classifiers that do not use inter-dependencies. The performance of our system on multi-localized proteins is comparable to a top performing system (YLoc + ), without restricting predictions to be based only on location-combinations present in the training set.

Keywords

Bayesian Network Multiple Location Location Prediction Location Indicator Bayesian Network Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Ramanuja Simha
    • 1
  • Hagit Shatkay
    • 1
    • 2
    • 3
  1. 1.Department of Computer and Information SciencesUniversity of DelawareNewarkUSA
  2. 2.Center for Bioinformatics and Computational Biology, DBIUniversity of DelawareNewarkUSA
  3. 3.School of ComputingQueen’s UniversityKingstonCanada

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