Figure 2.

Methods of network inference in uncharacterized prokaryotes. (a, b) Conventionally used methods for network reconstruction. (a) Orthology detection by comparison of transcription factor-target (TF-TG) links between species. Crosses indicate links known from the first species that are not found in the second species. (b) Position-specific weight matrices (PWMs) or hidden Markov models (HMMs) derived from binding site alignments (represented here by a grid) are used to predict target genes for conserved transcription factors. (c, d, e) The three recently published approaches to network reconstruction discussed here [7-9]. (c) The approach of Baumbach et al. [7]. (d) The approach of Balazsi et al. [8]. (e) The approach of Guo et al. [9]. Refer to the text for details of each of the studies (c-e) aimed at reconstructing actinobacterial transcription regulatory networks. Pol, polymerase; TFBS, transcription factor binding site.