Fig. 3

A heatmap of average logFC detected by DESeq2, EdgeR and Limma for 11 transcription factor genes (rows) for which its gene count is significantly correlated with anthocyanin content. Tissue1 and Tissue2 indicate the color of the callus/tissue sample used to perform differential expression analyses. The abbreviation, 44, NB and SB, indicate the cultivar CH5544, Nightbird and Superblack, respectively. For CH5544, the age of the samples are indicated as 6wks, 10wks, and 12wks, indicating 6, 10 and 12 weeks after sowing, respectively. For taproots of each cultivar, the results are summarized as outer/middle and inner/middle tissue comparisons, except for Superblack (SB), in which only outer and inner tissues were compared. A positive or negative number in each cell indicates that a gene was up- or downregulated in purple/slightly green tissue or calli. NA indicates that genes were not differentially expressed by any of the Bioconductor packages used in this study