I'm currently working with some computational models of bacteria. The bacterium I am considering is an Ecoli K-12 which has 139 genes. I have several models of the same bacterium with different combinations of genes that are active. e.g. M1 - M3 are the models and G1 - G4 are the genes. 1 indicates the gene is active and 0 inactive.
M G1 G2 G3 G4 M1 1 1 1 1 M2 1 0 1 0 M3 0 0 1 1
My assumption is that bacteria have a fixed number of chromosomes and randomly genes get activated. I intend to compute a similarity score between each pair of models (how similar two models are). I want to know what similarity means in terms of biology. Is a gene being active (1) considered a similarity or begin active and inactive (1 and 0)? For example if I compare M2 and M3 which similarity would be correct?
- 1 similarity (only G3 is active)
- 2 similarities (G3 is active and G2 is inactive)