Current Status of Pathway Finding Methods based on Gene Expression Data and Their Application

Abstract

DNA microarray technique is widely used to measure expressions of thousands of genes simultaneously. Data from this technique have a unique form; the number of parameters (genes) is huge whereas the number of measuring conditions (such as patients, time points, and cell lineages) is relatively small. Accordingly, data processing should be performed carefully. In particular, a method to narrow down the number of candidate genes is important to obtain meaningful results. In this paper, such techniques are discussed from different perspectives. First, a method to extract differentially expressed genes, which are the candidates of responsible genes, is introduced. In this method, a threshold for differential expression is determined depending on an expression level of each gene. Then some methods to find pathways, which show chemical relationships between genes, responsible for the differences in expression are described with an example from ventilator-associated lung injury.