5 for both channels. 230 genes fulfilled these criteria. For these 230 genes 444 time points showed an M value of ≥ 2 or ≤ -2. In testing these time points for an FDR (False Discovery Rate) corrected P value of ≥ 0.05, only 4 results (≈ 0.9%) were above this value. These were: t3 smc01523 P = 0.07, t33 smc04173 P = 0.09, t63 smb21026 P = 0.06, and t63 sma1736 P = 0.22. For K means clustering analysis of the microarray experiment data the Genesis software was used (Sturn, 2001; http://genome.tugraz.at/genesisclient/genesisclient_description.shtml). Alpelisib price The K means clustering was carried out in 8 groups. Acknowledgements This work was performed in the framework of project QLK3-CT-2002-02097 funded
by the commission of the European Communities. We thank Anke Becker for the possibility to use the Sm6kOligo microarrays and the analysis environment as well as Victoria Gödde and Manuela Meyer for the excellent technical support. Electronic supplementary material Additional file 1: Heat map of cluster A. By see more K-means Selleckchem EVP4593 the transcriptional data obtained by microarray analysis of the S. meliloti 1021 pH shock time course experiment were grouped into eight clusters.
In cluster A, genes exhibiting a strong and permanent induction were accumulated. Genes in this cluster remained up-regulated for the whole observation period. Presumably, these genes have a special impact for S. meliloti in facing low pH conditions. Each column of the heat map represents one time point after shift from pH 7.0 to pH 5.75 in the following order: 3, 8, 13, 18, 33, and 63 minutes. The values in the boxes are the M-values of a specific gene represented in a row. The background colour visualises the strength of the induction/lower expression (red/green) Florfenicol by the colour intensity. (JPEG 109 KB) Additional file 2: Heat map of cluster B of the eight clusters calculated by K-means clustering of the transcriptional data obtained by microarray analysis of the S. meliloti 1021 pH shock time course experiment. Cluster B is the largest cluster. The genes in this cluster are permanently up-regulated in response to the pH shift. It
contains exo genes responsible for the biosynthesis of succinoglycan and several genes which are rpoE2 dependently regulated. Among the genes in cluster B several encode for hypothetical proteins. Each column of the heat map represents one time point after shift from pH 7.0 to pH 5.75 in the following order: 3, 8, 13, 18, 33, and 63 minutes. The values in the boxes are the M-values of a specific gene represented in a row. The background colour visualises the strength of the induction/lower expression (red/green) by the colour intensity. (JPEG 574 KB) Additional file 3: Heat map of cluster C of the eight clusters calculated by K-means clustering of the transcriptional data obtained by microarray analysis of the S. meliloti 1021 pH shock time course experiment.