The results of all 20 combinations, in each of the nine experimental set-ups described in Table 16, are provided in Additional file 3. The impact on performance of individually selecting a particular pre-processing analytic or enabling a specific post-processing heuristic can be easily observed from this file.
The corresponding data is provided in the File S2, PFMs from TRANSFAC®, however, are removed from this file since they are proprietary.
The discretized gene-sample data can be reordered using spectral analysis [16], but if a gene-cluster really behaves co-ordinately the samples can be grouped simply by selecting these genes from this file and summing the columns, to reveal the mean number of genes "off" or "on" in every sample.
From this file, we extracted the phenotypes associated with mutants of genes present in the model.
A Perl script was then used to randomly select 1000 unique SNPs from this file.
Totally, 4123 genes with phenotypic information were extracted from this file.
Most information in other supplemental Tables is derived from this file to facilitate further data mining.
From this file, we decided to extract codes about "reviewed" proteins and extracted information from each species.
From this file, 10, 20, 40, 80, and 160 million alignments were randomly sampled to create a series of BAM files that increase in alignment size exponentially.
