Identification of Differentially Expressed and Co-Expressed Genes in High-Throughput Gene Expression Experiments

In recent years, a number of novel biotechnologies have enabled biologists to readily monitor genome-wide expression levels. For instance, microarray experiments provide high-throughput assays for measuring the abundance of deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) in different types of cell samples for thousands of sequences simultaneously (Phimister and Cohen, 1999; Packer, 2002; Packer and Axton, 2005; Speed, 2003). The microarray technology is being applied increasingly in biological and medical research to address a wide range of problems, such as the classification of tumors or the study of host genomic responses to bacterial infections (Alizadeh et al., 2000; Barrier et al., 2005a,b,c, 2006; Birkner et al., 2005a; Blanchette et al., 2005; Boldrick et al., 2002; Callow et al., 2000; Cawley et al., 2004; Chiappini et al., 2006; Chiaretti et al., 2004; DeSantis et al., 2005; Dudoit et al., 2002, 2003, 2006; Ge et al., 2003; Golub et al., 1999; Kele¸s et al., 2006; Pollard et al., 2005b; Pollard and van der Laan, 2004).