Exploration and analysis of R-loop mapping data with RLBase.

Miller, Henry E; Montemayor, Daniel; Li, Janet; Levy, Simon A; Pawar, Roshan; Hartono, Stella; Sharma, Kumar; Frost, Bess; Chedin, Frédéric; Bishop, Alexander J R

Miller, Henry E; Montemayor, Daniel; Li, Janet; Levy, Simon A; Pawar, Roshan; Hartono, Stella; Sharma, Kumar; Frost, Bess; Chedin, Frédéric; Bishop, Alexander J R.

Afiliación

Miller HE; Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA.
Montemayor D; Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA.
Li J; Bioinformatics Research Network, Atlanta, GA 30317, USA.
Levy SA; Department of Medicine, UT Health San Antonio, San Antonio, TX 78229, USA.
Pawar R; Center for Precision Medicine, UT Health San Antonio, San Antonio, TX 78229, USA.
Hartono S; Bioinformatics Research Network, Atlanta, GA 30317, USA.
Sharma K; Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T 1Z2, Canada.
Frost B; Canada's Michael Smith Genome Sciences Center, BC Cancer Research, Vancouver, BC V5Z 1L3, Canada.
Chedin F; Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA.
Bishop AJR; Bioinformatics Research Network, Atlanta, GA 30317, USA.

Nucleic Acids Res ; 51(D1): D1129-D1137, 2023 01 06.

Article en En | MEDLINE | ID: mdl-36039757

RESUMEN

R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. In 2012, Ginno et al. introduced the first R-loop mapping method. Since that time, dozens of R-loop mapping studies have been conducted, yielding hundreds of publicly available datasets. Current R-loop databases provide only limited access to these data. Moreover, no web tools for analyzing user-supplied R-loop datasets have yet been described. In our recent work, we reprocessed 810 R-loop mapping samples, building the largest R-loop data resource to date. We also defined R-loop consensus regions and developed a framework for R-loop data analysis. Now, we introduce RLBase, a user-friendly database that provides the capability to (i) explore hundreds of public R-loop mapping datasets, (ii) explore R-loop consensus regions, (iii) analyze user-supplied data and (iv) download standardized and reprocessed datasets. RLBase is directly accessible via the following URL: https://gccri.bishop-lab.uthscsa.edu/shiny/rlbase/.

Asunto(s)

Bases de Datos Genéticas; Estructuras R-Loop; ADN/genética; ADN/química; Hibridación Genética; Hibridación de Ácido Nucleico; ARN/genética; ARN/química

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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Bases de Datos Genéticas / Estructuras R-Loop Idioma: En Revista: Nucleic Acids Res Año: 2023 Tipo del documento: Article Pais de publicación: Reino Unido

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