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The coverage of each gene was calculated with 'BEDtools coverage' in BEDtools suite version 2.17.075.
Images were processed using the Leica application suite (version 2.8.1).
A homology model of VC0395_0300 was constructed using the Modeller Suite (Version 9.1).
We used version 3.3.4.6 of FFTW3, and compiled all codes with the GNU compiler suite, version 5.2.0, with '-O3' optimization.
In the suite version of compliance software, all of this information is known because one company controls all applications.
Data analyses were performed using Partek® Genomics Suite Version 6.4.
Calculation was done with the Prism software suite, version 5.01 (Graphpad, La Jolla, USA).
Spearman rank correlation between CAD-index and gene expression was calculated (Partek Genomics Suite Version 6.3).
Pair-wise scatter plots of replicate samples were generated by Partek Genomics Suite (Version 6.3).
Diffraction data were processed using the HKL program suite version 1.97.8 [27].
Affymetrix Microarray Suite version 5.0 was used to quantify each chip.
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