Regulatory networks. (A) Protein–DNA and protein–protein interaction network involving regulatory TFs and their target genes. (B) Protein–RNA, protein–protein, and microRNA–RNA interaction network involving RNA binding proteins and their target mRNAs and microRNAs and their target mRNAs. (C) Transcription regulatory networks. The transcriptional consequences of the protein interactions shown in A are included. (D) Post-transcription regulatory networks. The effects of the protein interactions shown in B on target gene expression are included. (E) Combined transcription and post-transcription regulatory networks. Red nodes, TFs; blue nodes, target genes; green node, a gene can be a target gene and encode a TF; yellow nodes, RNA binding proteins; purple nodes, microRNAs. Black edges, protein–DNA interactions; dashed edges, protein–RNA interactions; red edges, microRNA–RNA interactions; blue edges, protein–protein interactions. Arrows, activation; blunt “arrow,” repression.
