The Agilent dual color microarray employs a competitive binding of, respectively, a Cy3-labeled treatment sample and a Cy5-labeled mouse liver reference standard (a pool of three WT/LFD samples), which is presented as a Cy3/Cy5 binding ratio. The WT/LFD Cy5 binding provides the reference level of expression of each gene. We have considered genes that exhibit a WT/LFD Cy5 binding >200. This cutoff includes over 5,000 liver genes and greatly reduces false positives that readily appear as expression nears background. We further considered the relevant expression differences between the treatment groups to be two-fold or greater with p<0.05 (Table S2). This is based on the Limma program that tests significance in these array comparisons based on ANOVA [28]. The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE53910 (http://www.ncbi.nmk.nih.gov/geo/query/acc.cgi?acc=GSE53910).
