TRANSFAC

TRANSFAC provides a curated database of eukaryotic transcription factors, their DNA-binding sites, nucleotide distribution matrices, regulated genes, and tools for matrix-based binding site searches to support analysis of transcriptional regulation.

Key Features:

• Extensive Data Collection: Contains detailed information on transcription factors from multiple eukaryotic organisms including human, mouse, Drosophila, and Arabidopsis, with annotated binding sites and regulated genes.
• Nucleotide Distribution Matrices: Stores nucleotide distribution matrices (position weight/frequency matrices) for transcription factor binding sites.
• Match Tool and Match Profiler: Supports matrix-based searches of transcription factor binding sites with tissue- or state-specific profiles and allows creation and modification of these profiles via Match Profiler.
• Patch Tool: Performs complex queries across the database.
• Gene Linkages and Annotations: The GENE table links entries to LocusLink, RefSeq, OMIM, Ensembl, UniGene, EntrezGene, HumanPSD, and TRANSPRO, and includes standard gene names from HGNC, MGI, and RGD.
• Domain Assignments: Automatically assigns domains to transcription factor protein sequences using InterProScan, Pfam, SMART, and PROSITE.
• Complementary Databases and Modules: Includes TRANSCompel for composite elements, CYTOMER for anatomical and developmental data, TRANSPATH for signal transduction pathways, and the TRANSFAC Saccharomyces Module (TSM) for yeast data.

Scientific Applications:

• Regulatory Element Identification: Identification and analysis of potential transcription factor binding sites using matrix-based searches and nucleotide distribution matrices.
• Expression Pattern Prediction: Prediction and comparison of gene expression-regulatory patterns across tissues and developmental stages using tissue- or state-specific profiles.
• Gene Regulation Research: Hypothesis generation and testing in studies of gene regulatory mechanisms, including disease modeling and therapeutic target investigation.
• Network and Systems Biology: Construction and analysis of transcriptional regulatory networks and integration with signal transduction and anatomical/developmental data.

Methodology:

Matrix-based binding site searches and profile creation/modification are performed with the Match Tool and Match Profiler; complex queries use the Patch Tool; automatic domain assignment to protein sequences is performed using InterProScan, Pfam, SMART, and PROSITE; nucleotide distribution matrices are provided for binding-site representation.