Clusters 7 and 8 were not included as they consisted of less than four proteins. The differentially expressed proteins were organized into 10 clusters by K-means clustering. Temporal clustering during spore germination and outgrowth. Functional categories were obtained from SubtiWiki20. The black dashed line represents the zero level. The trends for proteins represent the changes in the protein levels relative to those in the vegetative cells. The light color represents the individual genes (red) and proteins (blue), whereas the dark color indicates the median Z-scores for the set of genes and proteins across all the time points. (B) Trends are shown for the differentially expressed mRNA and proteins belonging to the functional categories peptidoglycan biosynthesis ( n = 8) fatty acid synthesis ( n = 8) cell division and cell shape ( n = 7) DNA replication, processing, and repair ( n = 5) and membrane proteins and transporters ( n = 69 and 21, respectively). Functional categories were obtained from SubtiWiki. The light colors in the protein profiles correspond to the individual proteins, whereas the dark colors indicate the median Z-score profiles obtained by approach I (see Materials and Methods for details). The heat map for gene expression profiles shows the results of analysis of the behavior of individual genes in the various samples versus a common reference (pool of all samples see Materials and Methods for details). The columns represent the different time points corresponding to dormant to outgrowing spores. (A) The Z-score transformed profiles of the genes (rows in the heat map) and corresponding proteins are shown. Functional categories and expression patterns of the differentially expressed genes and proteins during germination and outgrowth of B.
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