Factor-dependency analysis for GRNs inferred from experimental data sets. (A) Schematic diagram of the factor-dependency analysis. Three factors that affect the accuracy of the inferred network were analyzed, i.e., the dynamics of the TF, the expression level of the target gene (pre-mRNA or mRNA), and the mRNA half-life of the target gene. (B) The dependency of the network inference accuracy on mRNA (or pre-mRNA) expression levels of target genes in four data sets. The dependency was quantified by using the P-value as in Supplemental Figure S7A, calculated by comparing the inference accuracies between targets of low or high expression levels for each network. Horizontal dashed line indicates P = 0.05. (C) Analogous to (B) for the mRNA half-life of the target gene. (D) The dependency of the network inference accuracy on the TF dynamics. The dynamics of TFs were approximated by using cell-to-cell variabilities of TF activities measured by public single-cell ATAC-seq data (Methods). TFs from all four data sets were sorted according to TF dynamics, and the fraction of TFs more accurately inferred by the pre-mRNA-based method than by the mRNA-based method was calculated for TFs above the indicated value of TF dynamics on the x-axis (see also Supplemental Fig. S7B,C).