Comparing the distribution of expression and network coherence for single- and multi-species methods for the B. subtilis - B. anthracis pairing. A comparison of the expression and network coherence for the different MS and SS methods. For brevity, we present here only the results from full data methods (FD) from the B. subtilis-B. anthracis pairing (the results for the other pairings and expression only (EO) methods can be found in Additional file 1). Abbreviations are given for each method; a key to these abbreviations can be found in Table 1. Across the three comparisons, no method outperformed all other methods as judged by all three metrics, with the MSCM results performing competitively with the others. (a) The distributions of the residual values from each method for the pairing of B. subtilis and B. anthracis. We also show, next to each distribution (in gray), the residuals from randomly shuffled (bi)clusters that match the size distribution for each method with n = 1000 for the number of copies of the original set of (bi)clusters (same number of genes, conditions and (bi)clusters). Most methods tested were significantly better than random for both organisms; the exceptions being MSISA, QUBIC, and Coalesce (COAL). In addition, this plot illustrates the tendency of MSKM to allow an organism with a considerably larger expression dataset to dominate the analysis. (b) The distributions of the average absolute correlation from each method for the pairing of B. subtilis and B. anthracis are displayed to allow comparison between methods that identify inversely correlated biclusters (MSISA, QUBIC) and those that do not. As in (a), we also display the results from a randomly shuffled distribution next to each method in gray (n = 1000). In all cases, with the exception of QUBIC for B. subtilis, the method was significantly higher than random. (c) The distributions of the association P-values (-log10) from each method compared.