title: Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations.
abstract: 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.
authors.affiliation: Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada.
authors.forename: Duane
authors.initials: D
authors.lastname: Szafron
authors.forename: Paul
authors.initials: P
authors.lastname: Lu
authors.forename: Russell
authors.initials: R
authors.lastname: Greiner
authors.forename: David S
authors.initials: DS
authors.lastname: Wishart
authors.forename: Brett
authors.initials: B
authors.lastname: Poulin
authors.forename: Roman
authors.initials: R
authors.lastname: Eisner
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Lu
authors.forename: John
authors.initials: J
authors.lastname: Anvik
authors.forename: Cam
authors.initials: C
authors.lastname: Macdonell
authors.forename: Alona
authors.initials: A
authors.lastname: Fyshe
authors.forename: David
authors.initials: D
authors.lastname: Meeuwis
mesh_terms: D020407:Internet; D011506:Proteins / Q000145:classification / Q000502:physiology; D020543:Proteome / Q000737:chemistry*; D040901:Proteomics; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins; D020543:Proteome