Scatterplot of fold changes for the 2889 orthologous genes in D. dadantii vs P. atrosepticum. Fold change values are represented as log ratio of expression in anaerobic vs. aerobic condition. The categories represented are: Statistically significant up-regulation with fold changes greater than 3 (log2 > 1.5) in both organisms (orange box), Statistically significant down-regulation with fold changes greater than 3 (log2 > 1.5) in both organisms (purple box), Statistically significant expression in both organisms but in opposite directions (up-regulated in D. dadantii: green box, down-regulated in D. dadantii: brown box) and Equivalently expressed in both organisms (black). At least 81 genes are part of a highly differentially regulated core of genes conserved across D. dadantii and P. atrosepticum (orange and purple boxes) and this minimum core grows to 222 genes if we allow smaller, but statistically significant differences between aerobic and anaerobic samples (red and blue filled circles). We observe divergent expression patterns in which orthologs are up-regulated > 3- fold in one organism and down-regulated > 3- fold (log2 > 1.5) in the other organism for 15 ortholog sets (brown and green boxes), and at least 35 additional ortholog sets show a less extreme, but nevertheless divergent pattern (brown and green filled triangles). Genes that are differentially expressed in one organism only, have not been distinguished in the figure. Given the overall larger number of genes called differentially expressed for D. dadantii relative to P. atrosepticum, there are many cases where the ortholog in one organism is called differentially expressed (and with fold change > 3), while the ortholog in the other genome is not (966 ortholog groups in D. dadantii and 77 different groups in P. atrosepticum). In most cases both members of the ortholog group trend in the same direction (766 orthologs) rather than exhibiting divergent expression (277 orthologs).
Babujee et al. BMC Genomics 2012 13:110 doi:10.1186/1471-2164-13-110