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CDH1, ERBB3 and ZEB1 signatures were generated by Partek Genomic Suites version 6.6 by using Student's t-test with FDR of 0.05.
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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.
The SAMtools suite (version 0.1.18) (Li et al. 2009) with default settings was used to call SNVs and short INDELS per variety.
Data analyses were performed using Partek® Genomics Suite Version 6.4.
NMR resonances of metabolites were assigned using the Chenomx NMR Suite (version 5.0; Chenomx Inc., Edmonton, Canada).
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).
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