Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 Page 7 of 17 Figure 3 Heat map comparison of the core genome, pan-genome, and Bacillus groups conservancy of COGs. Normalized Cluster of Orthologous Groups (COGs) frequencies within each group are shown as a two way clustering; interestingly the clustering supports the groups formed in the core genome phylogeny (horizontal axis). In vertical axis COGs are grouped according to their abundance showing moderate conserved COGs in the top, low frequency conserved COGs in the central clusters and highly abundant COGs cluster in the lower clusters. In the bottom total numbers of proteins families mapped to COG within each row are shown. Some categories are at least partially over-represented in the core when compared to the pan-genome and to either group and include the following: COG H (coen- zyme transport and metabolism; core = 0.05/pan-gen- ome = 0.03), which includes biosynthesis genes for biotin (birA), riboflavin (ribA), co-enzyme A (ylol), and a dipicolinate synthase (spoVFB); COG F (nucleotide transport and metabolism; core = 0.05/pan-genome = 0.03), which includes comEB competence protein; COG O (protein turnover and chaperones; core = 0.05/pan- genome = 0.03), which includes genes such as groES; and COG D (cell division), which includes the DNA translocase ftsK, the rod shape-determining gene rodA, and some sporulation-related genes such as spoIID, spoVE, and soj. COG categories U (intracellular trafficking and secre- tion), N (cell motility), and I (lipid transport) are in the same range and the fractional differences between the core, pan-genome, and Bacillus groups of these cate- gories are not noticeable (average = 0.01). Categories K (transcription; core = 0.06/average = 0.09) and S (gen- eral functions; core = 0.06/average = 0.09) are underre- presented in the core. Despite the ubiquity of these genes within Bacillus, there are only a few transcription- related proteins that are shared between all of them. It has been shown, however, that a given transcription fac- tor ortholog selected solely by RBH may not have a con- served function, and this aspect depends on the phylogenetic distance and tempo of the rapidly evolving regulatory networks [42]. We expected and observed