Rank discriminants for predicting phenotypes from RNA expression

Bahman Afsari, Ulisses M. Braga-Neto, Donald Geman

Research output: Contribution to journalArticle

Abstract

Statistical methods for analyzing large-scale biomolecular data are commonplace in computational biology. A notable example is phenotype prediction from gene expression data, for instance, detecting human cancers, differentiating subtypes and predicting clinical outcomes. Still, clinical applications remain scarce. One reason is that the complexity of the decision rules that emerge from standard statistical learning impedes biological understanding, in particular, any mechanistic interpretation. Here we explore decision rules for binary classification utilizing only the ordering of expression among several genes; the basic building blocks are then two-gene expression comparisons. The simplest example, just one comparison, is the TSP classifier, which has appeared in a variety of cancer-related discovery studies. Decision rules based on multiple comparisons can better accommodate class heterogeneity, and thereby increase accuracy, and might provide a link with biological mechanism. We consider a general framework (“rank-in-context”) for designing discriminant functions, including a data-driven selection of the number and identity of the genes in the support (“context”). We then specialize to two examples: voting among several pairs and comparing the median expression in two groups of genes. Comprehensive experiments assess accuracy relative to other, more complex, methods, and reinforce earlier observations that simple classifiers are competitive.

Original languageEnglish (US)
Pages (from-to)1469-1491
Number of pages23
JournalAnnals of Applied Statistics
Volume8
Issue number3
DOIs
StatePublished - Sep 1 2014

Keywords

  • Cancer classification
  • Gene expression
  • Order statistics
  • Rank discriminant

ASJC Scopus subject areas

  • Statistics and Probability
  • Modeling and Simulation
  • Statistics, Probability and Uncertainty

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