Methods for monitoring multiple gene expression

A method for monitoring differential expression of a plurality of genes in a first Bacillus cell relative to expression of the same genes in one or more second Bacillus cells, comprising:

• (a) adding a mixture of labeled nucleic acid probes isolated from the first Bacillus cell and the one or more second Bacillus cells to a substrate containing an array of Bacillus licheniformis genomic sequence tags (GSTs) under stringency conditions where the nucleic acids hybridize to complementary sequences of the Bacillus licheniformis GSTs in the array, wherein the nucleic acids from the first Bacillus cell and the one or more second Bacillus cells are labeled with a first reporter and one or more different second reporters, respectively, wherein the Bacillus licheniformis GSTs are selected from the group consisting of SEQ ID NOs. 1-4448, and wherein the stringency conditions are high or very high stringency conditions, and wherein the array contains SEQ ID NO.322;
• and
• (b) examining the array under conditions wherein the relative expression of the genes in the Bacillus cells is determined by the observed hybridization reporter signal of each spot in the array in which (i) the Bacillus licheniformis GSTs in the array that hybridize to the nucleic acids obtained from either the first Bacillus cell or the one or more second Bacillus cells produce a distinct first hybridization reporter signal or one or more second hybridization reporter signals, respectively, and (ii) the Bacillus licheniformis GSTs in the array that hybridize to the nucleic acids obtained from both the first and one or more second Bacillus cells produce a distinct combined hybridization reporter signal.