Assessing key decisions for transcriptomic data integration in biochemical networks
Fig 1
Formulation and implementation of preprocessing decisions.
(A) Two types of gene mapping methods (GM1 and GM2) are compared. (B) Two types of thresholding approaches (global and local) are compared. (C) Formulation of three combinations of number of states (Global T1, Local T1, and Local T2) (D) Decisions about the order in which thresholding and gene mapping are performed. For Order 1, gene expression is converted to reaction activity followed by thresholding of reaction activity; for Order 2, thresholding of gene expression is followed by its conversion to reaction activity.