Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression.

The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw/) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and other important regulatory elements (CpG islands and tandem repeats) in a promoter or a set of promoters in plants. Additionally, TFBSs, CpG islands, and tandem repeats in the conserve regions between homologous gene promoters are also identified. The current PlantPAN release (version 2.0) contains 16,960 TFs and 1,143 matrices of TF binding sites among 76 plant species. Besides update of the annotation information, adding experimentally verified TF matrices, and improvements in visualization of transcriptional regulatory networks, several new features and functions were first incorporated.

These features include: (i) comprehensive curation of TF information (response conditions, target genes, and sequence logos of binding motifs, etc.), (ii) co-expression profiles of TFs and their target genes under various conditions (i.e., environmental stresses, hormone treatments, and developmental stages), (iii) protein-protein interactions among TFs and their co-factors, (iv) TF-target networks, and (v) downstream promoter elements. Furthermore, a dynamic transcriptional regulatory network under various conditions is first provided in plant resources. The PlantPAN 2.0 is the most systematic platform for plant promoter analysis and reconstructing transcriptional regulatory networks.