TDTHub

TDTHub provides analysis of transcription factor binding sites (TFBSs) across plant species to identify regulatory elements and transcriptional regulators involved in gene expression control.

Key Features:

• Pre-computed TFBS datasets for 40 plant species: Provides genome-wide, pre-computed TFBS data covering 40 different plant species for comparative TFBS analysis.
• Two mapping algorithms: Offers two distinct mapping algorithms for TFBS detection and locus mapping.
• TFBS enrichment analysis: Performs TFBS enrichment analysis to detect over-represented motifs in query gene sets or regions.
• Integrated analysis and visualization tools: Includes tools for downstream data analysis and visualization of regulatory relationships and results.
• Demonstrated biological applications: Applied to anthocyanin biosynthesis and to jasmonate- and wounding-responsive transcriptional cascades in Arabidopsis thaliana and Solanum lycopersicum (tomato), identifying known and candidate TF nodes.

Scientific Applications:

• Regulatory network inference: Identification of transcription factors and TFBSs that define regulatory interactions driving gene expression changes.
• Pathway-specific regulation: Analysis of transcriptional regulation in metabolic pathways such as anthocyanin biosynthesis.
• Stress and signaling responses: Investigation of jasmonate- and wounding-responsive transcriptional cascades in Arabidopsis thaliana and Solanum lycopersicum (tomato).
• Comparative genomics: Comparative TFBS analysis across multiple plant species using pre-computed datasets.

Methodology:

Uses pre-computed TFBS datasets for 40 plant species, applies two distinct mapping algorithms for TFBS mapping, and performs TFBS enrichment analysis with integrated data-analysis and visualization tools.