GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments
Ivan Yevshin1,2, Ruslan Sharipov1,2,3, Tagir Valeev1,4
1BIOSOFT.RU, LLC, Novosibirsk 630058, Russian Federation.
Nucleic Acids Research
|December 8, 2016
Summary
The Gene Transcription Regulation Database (GTRD) consolidates transcription factor binding sites (TFBSs) from ChIP-seq experiments. It offers a unified resource for TFBS data, aiding gene regulation research.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Transcription factors (TFs) play a crucial role in gene regulation by binding to specific DNA sequences.
- Identifying transcription factor binding sites (TFBSs) is essential for understanding gene expression patterns.
- Existing databases may lack comprehensive or uniformly processed TFBS data.
Purpose of the Study:
- To develop and present the Gene Transcription Regulation Database (GTRD), a centralized resource for TFBSs.
- To provide uniformly processed TFBS data derived from ChIP-seq experiments for human and mouse.
- To offer advanced search and visualization tools for exploring TFBS information.
Main Methods:
- Collected raw ChIP-seq data from ENCODE and SRA for human and mouse.
- Uniformly processed ChIP-seq data using Bowtie2 for alignment and MACS, SISSRs, GEM, PICS for peak calling.
- Merged peaks into clusters and subsequently into non-redundant metaclusters representing TFBSs.
- Developed a web interface using the BioUML platform for data access and analysis.
Main Results:
- Established GTRD, a comprehensive database of TFBSs identified through ChIP-seq.
- Integrated structured information on cell lines and experimental conditions for each TFBS.
- Implemented a user-friendly web interface with browsing, advanced search, and an integrated genome browser.
- Included visualization of read alignments, peaks, clusters, metaclusters, gene structures, and predicted binding sites.
Conclusions:
- GTRD provides a valuable, unified resource for researchers studying gene transcription regulation.
- The database facilitates the identification of genes regulated by specific transcription factors.
- Advanced search and visualization tools enhance the utility of GTRD for genomic research.
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