PlnTFDB

PlnTFDB catalogs transcription factors (TFs) and transcriptional regulators (TRs) across plant species, including unicellular algae and angiosperms, to support comparative and evolutionary analyses of gene regulatory networks spanning approximately 1.6 billion years.

Key Features:

• Putatively complete TF/TR sets: Provides putatively complete sets of TFs and TRs from 19 fully sequenced and annotated plant species.
• Family coverage: Covers 84 distinct families of transcription factors and transcriptional regulators across plant lineages.
• Gene family annotations: Supplies detailed gene family descriptions, literature references, and multiple sequence alignments of protein domains for each entry.
• Expressed sequence tags (ESTs): Provides ESTs associated with each TF or TR gene to support expression analyses.
• 3D protein structures: Offers 3D protein structures of homologous proteins where available for structural and modeling studies.
• Domain architecture: Includes domain architecture information to support functional annotation and evolutionary comparisons.
• Orthology links: Links species through orthologous genes to enable cross-species comparisons.
• Cross-resource integration: Integrates cross-links to other computational resources online.

Scientific Applications:

• Gene regulatory network analysis: Use the cataloged TFs and TRs to analyze regulatory networks in plants.
• Comparative genomics: Compare TF/TR repertoires across unicellular algae to angiosperms to study evolutionary trends.
• Functional annotation: Perform functional annotation and domain-based comparative studies using multiple sequence alignments and domain architectures.
• Structural biology and modeling: Conduct structural analyses and molecular modeling using available 3D homologous protein structures.
• Orthology-driven studies: Identify conserved regulatory mechanisms across species via orthologous gene links.

Methodology:

Provides multiple sequence alignments of protein domains; establishes links between species via orthologous gene assignments; maps to homologous proteins to associate available 3D structures.