PlantRegMap

PlantRegMap provides a database and analysis platform that maps plant transcription factors (TFs), cis-regulatory elements, and their functional interactions to support studies of transcriptional regulation and comparative genomics.

Key Features:

• Updated Transcription Factor Annotations: Updated annotations of transcription factors (TFs) collected across plant species.
• Extended TF Repertoires (TFext): TFext provides TF repertoires for newly sequenced plant species.
• Cis-Element Data and Functional Interactions: Regularly updated cis-element data and documented functional interactions between TFs and cis-elements.
• Genome-Wide Conservation Landscapes: Genome-wide conservation landscapes established for 63 representative plant species.
• FunTFBS Algorithm: FunTFBS screens for functional regulatory elements and interactions by integrating base-varied TF binding affinities with evolutionary footprints on binding sites, identifying over 20 million functional TF binding sites (TFBSs) and two million functional interactions among 21,346 TFs.
• Functional Regulatory Maps: Detailed functional regulatory maps for the 63 representative plant species derived from FunTFBS results and conservation landscapes.
• Origin (PlantTFDB): Extension of the TF-centered database PlantTFDB to broader regulatory annotations.

Scientific Applications:

• Decoding Transcriptional Regulatory Systems: Mapping TFs, cis-elements, and interactions to elucidate plant transcriptional regulatory networks.
• Comparative Genomics Studies: Using conservation landscapes across 63 species to compare regulatory element conservation and evolutionary patterns.
• Functional Genomics Research: Leveraging wide-scale TFBS and interaction data to investigate gene regulation and expression mechanisms.
• Plant Breeding and Biotechnology: Informing breeding and biotechnological strategies by identifying regulatory elements and TF interactions linked to traits.

Methodology:

Integration of updated TF annotations, establishment of genome-wide conservation landscapes for 63 species, and application of the FunTFBS algorithm that integrates base-varied TF binding affinities with evolutionary footprints to identify functional TFBSs and TF–target interactions.