PlantTFcat

PlantTFcat identifies and classifies plant transcription factors (TFs), transcriptional regulators (TRs), and chromatin regulators (CRs) from genome-scale protein and nucleic acid sequences using conserved domain patterns.

Key Features:

• Genome-scale sequence analysis: Performs analysis of genome-scale protein and nucleic acid sequences to detect regulatory elements.
• Systematic domain pattern analysis: Analyzes InterProScan domain patterns in protein sequences to detect conserved domains associated with TF/TR/CR families.
• Comprehensive prediction logics: Applies prediction logics derived from relationships between gene families and conserved domains across 108 published plant TF/TR/CR families to distinguish families that share conserved domains.
• High coverage and sensitivity: Demonstrates high coverage and sensitivity in annotating known TF/TR/CR families as determined by systematic performance evaluations.

Scientific Applications:

• Genomic Research: Enables identification of TFs, TRs, and CRs to support discovery of regulatory networks and pathways in plant genomes.
• Functional Genomics: Supports assignment of regulatory roles to genes by classifying transcription factors and regulators relevant to gene expression studies.
• Comparative Genomics: Provides consistent family-level categorizations to facilitate cross-species comparisons of transcriptional regulators.

Methodology:

Systematic analysis of InterProScan domain patterns in protein sequences combined with prediction logics based on conserved domain–gene family relationships across 108 published plant TF/TR/CR families, with performance assessed via systematic evaluations.