PlantTFDB 2.0

PlantTFDB 2.0 provides comprehensive annotations and classification of plant transcription factors, cataloging 53,319 putative TFs across 49 plant species and supplying domain annotations, gene ontology classifications, expression patterns, ortholog groups, cross-references, multiple sequence alignments, phylogenetic trees, and Weblogo visualizations to support studies of gene regulation, evolutionary biology, and functional genomics.

Key Features:

• Catalog: 53,319 putative transcription factors predicted across 49 plant species.
• Annotations: General information, domain characteristics, gene ontology classifications, expression patterns, and ortholog groups for each TF.
• Cross-references and literature: Cross-references to external databases and literature citations associated with TF entries.
• Family classification: Assignment of TFs into 58 families based on computational approaches and manual inspection.
• Comparative data: Multiple sequence alignments and phylogenetic trees for each TF family, provided as Weblogo pictures or downloadable text files.

Scientific Applications:

• Gene regulation: Supports analyses of transcription factor roles in plant gene regulation.
• Evolutionary biology: Enables study of TF family evolution and ortholog relationships across 49 species.
• Functional genomics: Facilitates annotation-driven functional interpretation using domain, expression, and gene ontology data.
• Comparative analyses: Allows comparative sequence and phylogenetic analyses using MSAs, phylogenies, and Weblogo visualizations.
• Plant genomics and molecular biology: Provides annotated TF data for plant genomics and molecular biology investigations.

Methodology:

Putative TFs were predicted using computational approaches; TF family classification employed computational approaches; multiple sequence alignments, phylogenetic tree construction, and Weblogo generation were produced.