Fig. 1

Gene neighborhood and gene function similarity. a Gene neighborhood. b Gene function similarity. a In this study, we looked at three genes in the upstream and downstream directions for neighboring genes of a given gene G. For a gene G, the neighboring gene at +2 is from an opposite strand upstream and genes colored in red are organized onto the same operon with the gene G. The functional relationship with neighboring genes within the neighborhood of [−3, 3] is integrated into the formula to calculate PAC where strand and operon information can be integrated into the Eq. (4) (described in Methods). b For a pair of two GO terms, function similarity (GOsim) measures how much detailed functional information (low-level GO terms on a GO graph) is shared. All dotted ovals represent GO terms assigned to genes where the +2 gene does not have a GO term assigned to it, such that GOsim(G₊₂, G) is not available. All ovals over the dotted ovals represent predecessor GO terms of assigned GO terms to genes excluding root GO terms on a GO graph. The ovals lined in black mean that corresponding GO terms do not occur, and the ovals lined in blue mean that corresponding GO terms occur in a set of predecessor GO terms of a given gene G