Target Explorer

Target Explorer identifies and annotates regulatory DNA sequences, including transcription factor binding sites (TFBS), and predicts putative target genes in eukaryotic genomes.

Key Features:

• Customized TFBS Libraries: Creation of custom position weight matrices or binding site matrices to represent transcription factor binding specificities.
• Cluster Prediction: Identification of clusters of TFBS that indicate candidate regulatory regions.
• Target Gene Identification: Prediction and annotation of putative target genes potentially regulated by identified transcription factors.
• Integration with Genome Annotations: Use of genome annotation context to inform and refine TFBS and target gene predictions.
• Automated Workflow: Automation of steps from binding site library creation through TFBS and cluster prediction to target gene annotation.

Scientific Applications:

• Drosophila melanogaster studies: Analysis of regulatory elements and transcription factor networks in the Drosophila melanogaster genome.
• Cross-species eukaryotic analysis: Application to other eukaryotic genomes for comparative regulatory investigations.
• Functional genomics: Exploration of gene regulation and assignment of regulatory elements to genes in functional genomics studies.
• Transcription factor network analysis: Investigation of interactions among transcription factors and their target genes.
• Regulatory element discovery in biological processes: Identification of novel regulatory elements relevant to development, disease, and evolutionary processes.

Methodology:

Computational TFBS prediction is integrated with genome annotation context and automated procedures for creating binding site matrices, predicting TFBS clusters, and annotating putative target genes.