Abstract
Genome-wide studies are fast becoming the norm, partly fueled by the availability of genome sequences and the feasibility of high-throughput experimental platforms, e.g., microarrays. An important aspect in any genome-wide studies is determination of regulatory relationships, believed to be primarily transacted through transcription factor binding to DNA. Identification of specific transcription factor binding sites in the cis-regulatory regions of genes makes it possible to list direct targets of transcription factors, model transcriptional regulatory networks, and mine other associated datasets for relevant targets for experimental and clinical manipulation. We have developed a web-based tool to assist biologists in efficiently carrying out the analysis of genes from studies of specific transcription factors or otherwise. The batch extraction and analysis of cis-regulatory regions (BEARR) facilitates identification, extraction, and analysis of regulatory regions from the large amount of data that is typically generated in genome-wide studies. This chapter highlights features and serves as a tutorial for using this publicly available software. The URL is http://giscompute.gis.a-star.edu.sg/R2vega/BEARR1.0/.
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Berlian Vega, V. (2006). cis-Regulatory Region Analysis Using BEARR. In: Bina, M. (eds) Gene Mapping, Discovery, and Expression. Methods in Molecular Biology, vol 338. Humana Press. https://doi.org/10.1385/1-59745-097-9:119
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DOI: https://doi.org/10.1385/1-59745-097-9:119
Publisher Name: Humana Press
Print ISBN: 978-1-58829-575-0
Online ISBN: 978-1-59745-097-3
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