PlantReg: the reconstruction of links between transcription factor regulatory networks and biological processes under their control

The description of the path from a gene to a trait, as the main task of many areas in biology, is currently being equipped with new methods affecting not only experimental techniques, but also analysis of the results. The pleiotropic effect of a gene is due to its participation in numerous biological processes involved in different traits. A widespread use of genome-wide sequencing of transcripts and transcription factor (TF) binding regions has made the following tasks relevant: unveiling pleiotropic effects of TFs based on the functions of their target genes; compiling the lists of TFs that regulate biological processes of interest; and describing the ways of TF functioning (their primary and secondary targets, higher order targets, TF interactions in the process under study). We have previously developed a method for the reconstruction of TF regulatory networks and proposed an approach that allows identifying which biological processes are controlled by these networks and how this control is exerted. In this paper, we have implemented the approach as PlantReg, a program available as a web service. The paper describes how the program works. The input consists of a list of genes and a list of TFs - known or putative transcriptional regulators of these genes. As an output, the program provides a list of biological processes enriched for these genes, as well as information about by which TFs and through which genes these processes are controlled. We illustrated the use of PlantReg deciphering transcriptional regulation of processes initiated at the early salt stress response in Arabidopsis thaliana L. With PlantReg, we identified biological processes stimulated by the stress, and specific sets of TFs that activate each process. With one of these processes (response to abscisic acid) as an example, we showed that salt stress mainly affects abscisic acid signaling and identified key TFs in this regulation. Thus, PlantReg is a convenient tool for generating hypotheses about the molecular mechanisms that control plant traits.