TFmapper: A Tool for Searching Putative Factors Regulating Gene Expression Using ChIP-seq Data.

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• Next-generation sequencing technologies like ChIP-seq, DNase-seq, and ATAC-seq generate vast amounts of data on gene expression regulation.
• Understanding the transcriptional and epigenetic control of gene expression requires tools to query these large datasets effectively.

Purpose of the Study:

• To develop a tool for simultaneous querying of multiple ChIP-seq, DNase-seq, and ATAC-seq datasets.
• To enable identification of regulatory factors, including transcription factors and epigenetic regulators, that target specific genes or genomic regions.

Main Methods:

• Annotation of thousands of ChIP-seq, DNase-seq, and ATAC-seq peaks from ENCODE, GEO, and Cistrome projects.
• Development of a MySQL database (TFmapper) to store annotations and metadata.
• Creation of a web interface for user-friendly searching and data visualization.

Main Results:

• TFmapper allows users to search across thousands of datasets using gene symbols or genomic coordinates.
• The tool identifies factors targeting a genomic region or gene of interest in a specified sample.
• Users can visualize multiple peaks in genome browsers and download corresponding sequences.

Conclusions:

• TFmapper facilitates the exploration of publicly available ChIP-seq, DNase-seq, and ATAC-seq data.
• The tool supports integrative analyses to understand gene regulation.
• TFmapper is accessible via a web server at http://www.tfmapper.org/.