TY - JOUR

T1 - BSXplorer: analytical framework for exploratory analysis of BS-seq data

AU - Yuditskiy, K.

AU - Bezdvornykh, I.

AU - Kazantseva, A.

AU - Kanapin, A.

AU - Samsonova, A.

N1 - Export Date: 21 March 2024 CODEN: BBMIC Адрес для корреспонденции: Samsonova, A.; Institute of Translational Biomedicine, Russian Federation; эл. почта: a.samsonova@spbu.ru Химические вещества/CAS: sulfite, 14265-45-3; hydrogen sulfite; Sulfites Сведения о финансировании: Russian Science Foundation, RSF, 23–14-00134 Текст о финансировании 1: This work is supported by the Russian Science Foundation Grant 23–14-00134 (K.Y, I.B, Alex K., A.S.).

PY - 2024/3/4

Y1 - 2024/3/4

N2 - Background: Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across divergent taxa, epigenetic inheritance and, eventually, phenotypic variation. Graphical representation of methylation data is crucial in exploring epigenetic regulation on a genome-wide scale in both plants and animals. This is especially relevant for non-model organisms with poorly annotated genomes and/or organisms where genome sequences are not yet assembled on chromosome level. Despite being a technology of choice to profile DNA methylation for many years now there are surprisingly few lightweight and robust standalone tools available for efficient graphical analysis of data in non-model systems. This significantly limits evolutionary studies and agrigenomics research. BSXplorer is a tool specifically developed to fill this gap and assist researchers in explorative data analysis and in visualising and interpreting bisulfite sequencing data more easily. Results: BSXplorer provides in-depth graphical analysis of sequencing data encompassing (a) profiling of methylation levels in metagenes or in user-defined regions using line plots and heatmaps, generation of summary statistics charts, (b) enabling comparative analyses of methylation patterns across experimental samples, methylation contexts and species, and (c) identification of modules sharing similar methylation signatures at functional genomic elements. The tool processes methylation data quickly and offers API and CLI capabilities, along with the ability to create high-quality figures suitable for publication. Conclusions: BSXplorer facilitates efficient methylation data mining, contrasting and visualization, making it an easy-to-use package that is highly useful for epigenetic research. © The Author(s) 2024.

AB - Background: Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across divergent taxa, epigenetic inheritance and, eventually, phenotypic variation. Graphical representation of methylation data is crucial in exploring epigenetic regulation on a genome-wide scale in both plants and animals. This is especially relevant for non-model organisms with poorly annotated genomes and/or organisms where genome sequences are not yet assembled on chromosome level. Despite being a technology of choice to profile DNA methylation for many years now there are surprisingly few lightweight and robust standalone tools available for efficient graphical analysis of data in non-model systems. This significantly limits evolutionary studies and agrigenomics research. BSXplorer is a tool specifically developed to fill this gap and assist researchers in explorative data analysis and in visualising and interpreting bisulfite sequencing data more easily. Results: BSXplorer provides in-depth graphical analysis of sequencing data encompassing (a) profiling of methylation levels in metagenes or in user-defined regions using line plots and heatmaps, generation of summary statistics charts, (b) enabling comparative analyses of methylation patterns across experimental samples, methylation contexts and species, and (c) identification of modules sharing similar methylation signatures at functional genomic elements. The tool processes methylation data quickly and offers API and CLI capabilities, along with the ability to create high-quality figures suitable for publication. Conclusions: BSXplorer facilitates efficient methylation data mining, contrasting and visualization, making it an easy-to-use package that is highly useful for epigenetic research. © The Author(s) 2024.

KW - Bisulfite sequencing

KW - Clustering

KW - DNA methylation

KW - Epigenomics

KW - Exploratory data analysis and visualization

KW - Gene body methylation

KW - Gene modules

KW - Methylation density

KW - Non-model organisms

KW - Alkylation

KW - Data handling

KW - Data mining

KW - DNA

KW - Gene encoding

KW - Gene expression

KW - Visualization

KW - Bisulfite-sequencing

KW - Clusterings

KW - DNA Methylation

KW - Exploratory data analyse and visualization

KW - Exploratory data analysis

KW - Gene module

KW - Model organisms

KW - Non-model organism

KW - Data visualization

KW - article

KW - bisulfite sequencing

KW - chromosome

KW - data analysis

KW - data mining

KW - epigenetics

KW - gene

KW - gene expression regulation

KW - gene regulatory network

KW - genomic instability

KW - inheritance

KW - methylation

KW - nonhuman

KW - phenotypic variation

KW - animal

KW - DNA sequencing

KW - genetic epigenesis

KW - genomics

KW - hydrogen sulfite

KW - sulfite

KW - Animals

KW - Epigenesis, Genetic

KW - Genomics

KW - Sequence Analysis, DNA

KW - Sulfites

UR - https://www.mendeley.com/catalogue/c39893f4-99ca-3a87-9767-a86535fbb375/

U2 - 10.1186/s12859-024-05722-9

DO - 10.1186/s12859-024-05722-9

M3 - статья

C2 - 38438881

VL - 25

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

IS - 1

M1 - 1

ER -