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Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program

Fig 2

Genome-wide partition of gene expression in five sectors based on SVD.

A) SVD components and describe baseline fractional expression and dependence with growth, respectively, and together explain most of the expression variance. B) The fractional expression of every gene as a function of growth rate can be approximated by a linear combination of these two components, with loadings a_i and b_i. We show two examples (purple circles denote the expression vector, while the black dots correspond to the two-component approximation; lines added to help visualization) with the same baseline (dashed line; same a_i) but whose expression increases (b_i>0) or decreases (b_i<0) with growth. Data in A) and B) corresponds to growth in limiting glucose. C) The baseline expression of a gene can change, or not, between two nutrient conditions. A gene is nonspecific if its baseline expression remains the same (similar a_i loadings) in at least half of the 15 possible pairwise nutrient comparisons, being specific otherwise. Within nonspecific genes the second loadings b_i‘s on each nutrient condition enable us to determine if the gene is positive (mostly b_i>0 in all six conditions), invariant (b_i~0) or negative (b_i<0) with respect to growth rate change. Specific genes can similarly be separated between repressed or activated. In this way, we can partition the genome into five sectors what generalizes the scheme discussed with PA data in a subset of yeast genes (Fig 1). See main text for more details.

doi: https://doi.org/10.1371/journal.pcbi.1007353.g002