Finally, we compare these scores with scores obtained with null sets of matched SNP sets to calculate an empirical P-value for each condition (see Supplementary Notes for algorithm details).
The statistical model considered in this work is the same as that outlined in previous works, and proceeds with analysis in two steps: for each trait considered, we first estimate the matrix of (co variances between phenotypes, and then we use it when estimating the SNP effects (see Supplementary Note S1 for mathematical details).
Supplementary Note 2. Urls for analysis programs.
The clustering procedure is repeated also for S.cerevisiae, this time merging the two datasets and choosing a lower threshold in order to make an unbiased comparison with previous results for E.coli (similar number of edges, see Supplementary Notes S1 for details).
All other parameters were varied over their full range to produce confidence intervals around our different scenarios (see the Supplementary Notes S2 for detailed information on sensitivity analysis and Table S1 for parameter ranges).
Additional file 2: Supplementary Note 1. Criteria for functional prediction algorithms and conservation scores.
However, these limitations aside, it is reasonable to posit that the transcriptome assembly generated here is relatively comprehensive based on the following lines of evidence (see supplementary note, Supplementary Material online, for details).
See Supplementary Notes S1 for details.
For E.coli, the clustered expression correlations reproduce faithfully a large part of the collection of PC, and the matching clusters-PC is quasi-monogamous (see Fig. 2 and Supplementary Notes S8 for details and statistics).
The semantic similarity measure of Fig. 6 is drawn from [45], and the associated p.value by means of a bootstrapping method, see again the Supplementary Notes S1 for full detail.
