Local Context Finder (LCF) reveals multidimensional relationships among mRNA expression profiles of Arabidopsis responding to pathogen infection

Torrey Mesa Research Institute, Syngenta Research and Technology, 3115 Merryfield Row, San Diego, CA 92121

Communicated by Frederick M. Ausubel, Harvard Medical School, Boston, MA, July 11, 2003 (received for review December 19, 2002)

Abstract

A major task in computational analysis of mRNA expression profiles is definition of relationships among profiles on the basis of similarities among them. This is generally achieved by pattern recognition in the distribution of data points representing each profile in a high-dimensional space. Some drawbacks of commonly used pattern recognition algorithms stem from their use of a globally linear space and/or limited degrees of freedom. A pattern recognition method called Local Context Finder (LCF) is described here. LCF uses nonlinear dimensionality reduction for pattern recognition. Then it builds a network of profiles based on the nonlinear dimensionality reduction results. LCF was used to analyze mRNA expression profiles of the plant host Arabidopsis interacting with the bacterial pathogen Pseudomonas syringae. In one case, LCF revealed two dimensions essential to explain the effects of the NahG transgene and the ndr1 mutation on resistant and susceptible responses. In another case, plant mutants deficient in responses to pathogen infection were classified on the basis of LCF analysis of their profiles. The classification by LCF was consistent with the results of biological characterization of the mutants. Thus, LCF is a powerful method for extracting information from expression profile data.

Footnotes

↵ * To whom correspondence should be addressed at the present address: Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, St. Paul, MN 55108. E-mail: katagiri{at}umn.edu.
↵ † Present address: Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, St. Paul, MN 55108.
Abbreviations: LCF, Local Context Finder; LLE, Locally Linear Embedding; SA, salicylic acid; JA, jasmonic acid; ET, ethylene.