PlantTFDB

PlantTFDB catalogs transcription factors (TFs) and transcriptional regulators (TRs) across 19 plant species representing 84 families, enabling exploration of plant gene regulatory networks across approximately 1.6 billion years of evolution.

Key Features:

• Comprehensive Coverage: Putatively complete sets of TFs and TRs from 84 families across 19 plant species, spanning unicellular red and green algae to angiosperms.
• Evolutionary Scope: Dataset spans an evolutionary timeline of approximately 1.6 billion years across diverse plant lineages.
• Gene Family Annotations: Each gene family entry includes basic descriptions, literature references, expressed sequence tags (ESTs), 3D protein structure references, and domain architecture.
• Protein Domain Alignments: Multiple sequence alignments of protein domains are provided for family and gene entries.
• Cross-Species Orthology: Genes are linked across species via orthologous relationships to support comparative analyses.
• Sequence Similarity Search: Sequence similarity queries are supported via BLAST for sequence-based identification and comparison.

Scientific Applications:

• Gene Regulatory Network Analysis: Enables study of the evolution and function of plant gene regulatory networks through curated TF and TR data.
• Comparative Genomics: Supports identification of conserved and divergent regulatory mechanisms using orthologous gene relationships across species.
• Functional Annotation: Assists functional annotation of plant TFs and TRs using ESTs, 3D protein structure information, domain architecture, and sequence alignments.

Methodology:

Data were curated and integrated from fully sequenced and annotated plant genomes and processed using BLAST searches and multiple sequence alignments of protein domains.