Figure 2

Illustration of our proposed modeling conception. Here, we aim to reconstruct a gene regulatory network consisting of 4 genes (dark blue) and 2 transcription factors (light gray). For simplicity, we assume that only one gene expression measurement was performed. The expression level of each gene is given in the gene nodes. (A) The GRN template: In this example, two genes possess at least one TF binding site in their regulatory region as indicated by 3 TF-gene interactions (purple). (B) In that case, there are 5 possible gene-TF interactions (i.e. model parameters β) in the network (dashed, orange). If available, we might consider prior knowledge on gene-TF interactions during inference (adaptive TILAR). (C) A possible inference result including 3 gene-TF interactions (solid, orange). Here, the model perfectly fits the data (e.g. "8" = 2.0·"4") with two nominal model parameters set to zero. (D) We can use the inferred model to derive gene-gene relationships from the edges between genes and TFs (gray). The benchmarking was conducted on such gene-gene interactions.