Schematics of gene regulation and regulatory inference methods. (A) Schematic diagram of molecular species involved in transcriptional regulation. (B) Schematics comparing conventional and proposed methods for gene regulatory network (GRN) inference. Conventionally, mRNA levels of transcription factors and target genes from scRNA-seq data are used to infer GRN (i.e., the mRNA-based method). In contrast, we propose to use mRNA levels of transcription factors and pre-mRNA levels of target genes for inferring GRN (i.e., the pre-mRNA-based method).