A proposed scheme of the core regulatory network of drug-induced molecular mechanisms and gene expression alterations in the striatum. Small nodes represent transcripts belonging to the identified gene expression patterns. The color of each node reflects its gene pattern membership: blue, A; yellow, B1; orange, B2; and red, B3. Thin blue edges between the nodes indicate a correlation between the expression profiles of two genes. Functional connections were implemented based on our results from literature mining, pharmacological experiments and in silico predictions of TFBSs. Large hexagonal nodes represent elements of drug-activated signaling pathways. Solid and dashed edges between the nodes indicate direct or indirect interactions, respectively, as suggested by the literature. A red node color and thin red edge indicate a pharmacologically verified connection (Figure 4). Green triangle nodes represent gene transcription regulatory elements. Thin green edges indicate positive detection of TFBSs in a promoter region of a particular gene. Transparent arrows suggest the influence of gene expression changes on addiction-related traits based on the correlations between the transcriptional and phenotypic response (Figure 1c, d; Additional file 9).