Identifying transcription factors (TFs) cooperation controlling target gene expression is still an arduous challenge. The accuracy of current methods at genome scale significantly drops with the increase in number of genes, which limits their applicability to more complex genomes, like animals and plants. Here, we developed an algorithm, TransDetect, able to predict TFs combinations controlling the expression level of a given gene. TransDetect was used to identify novel TFs modules regulating the expression of Arabidopsis phosphate transporter PHO1;H3 comprising MYB15, MYB84, bHLH35 and ICE1. These TFs were confirmed to interact between themselves and with the PHO1;H3 promoter. Phenotypic and genetic analyses of TF mutants enable the organization of these four TFs and PHO1;H3 in a new gene regulatory network controlling phosphate accumulation in zinc-dependent manner. This demonstrates the reliability of TransDetect to extract directionality in non-dynamic transcriptomes and to provide blueprint to identify gene regulatory network involved in a given biological process.