Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations
Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
* To whom correspondence should be addressed. Tel: +1 780 492 7760; Fax: +1 780 492 1071; Email paullu{at}cs.ualberta.ca
Correspondence may also be addressed to Duane Szafron. Email: duane{at}cs.uslberta.ca
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Received February 15, 2004; Revised April 19, 2004; Accepted May 5, 2004
Proteome Analyst (PA) (http://www.cs.ualberta.ca/~bioinfo/PA/) is a publicly available, high-throughput, web-based system for predicting various properties of each protein in an entire proteome. Using machine-learned classifiers, PA can predict, for example, the GeneQuiz general function and Gene Ontology (GO) molecular function of a protein. In addition, PA is currently the most accurate and most comprehensive system for predicting subcellular localization, the location within a cell where a protein performs its main function. Two other capabilities of PA are notable. First, PA can create a custom classifier to predict a new property, without requiring any programming, based on labeled training data (i.e. a set of examples, each with the correct classification label) provided by a user. PA has been used to create custom classifiers for potassium-ion channel proteins and other general function ontologies. Second, PA provides a sophisticated explanation feature that shows why one prediction is chosen over another. The PA system produces a Naïve Bayes classifier, which is amenable to a graphical and interactive approach to explanations for its predictions; transparent predictions increase the user's confidence in, and understanding of, PA.
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