PlantPAN 5.0: updated database for integrating multiomics evidence and exploring multilayered transcriptional regulatory networks in plants.

PlantPAN 5.0 expands its integrated multiomics promoter resource to 240 plant species, adding 71 040 transcription factor annotations and 7762 nonredundant binding matrices.

• Why it matters: Plant transcriptional regulation is shaped by layered evidence—cis-elements, TF binding, chromatin accessibility, methylation, and 3D interactions—yet existing tools are fragmented and hard to compare across conditions.
• What they did: The update enlarges genome and promoter annotations plus PCBase 3.0 ChIP-seq, and adds ATAC-seq, bisulfite-sequencing, and four Hi-C datasets for Arabidopsis thaliana, with Differential Analysis and new promoter modules.
• The result: Users can integrate TF binding, accessibility, methylation, and chromatin interaction topology to prioritize regulatory TFs, shared cis-elements, and predicted TFBSs, enabling large-scale local analyses via a Dockerized, privacy-preserving package.

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