UMMS Affiliation

Bioinformatics Core; Program in Molecular Medicine; RNA Therapeutics Institute; Garber Lab

Publication Date

2019-01-05

Document Type

Article

Disciplines

Amino Acids, Peptides, and Proteins | Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology | Genetic Phenomena | Genomics | Nucleic Acids, Nucleotides, and Nucleosides

Abstract

BACKGROUND: Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immunoprecipitation sequencing (CLIP-Seq) or RNA immunoprecipitation (RIP-Seq) sequencing, DNA accessibility by assay for transposase-accessible chromatin (ATAC-Seq), DNase or MNase sequencing libraries. The processing of these sequencing techniques involves library-specific approaches. However, in all cases, once the sequencing libraries are processed, the result is a count table specifying the estimated number of reads originating from each genomic locus. Differential analysis to determine which loci have different cellular activity under different conditions starts with the count table and iterates through a cycle of data assessment, preparation and analysis. Such complex analysis often relies on multiple programs and is therefore a challenge for those without programming skills.

RESULTS: We developed DEBrowser as an R bioconductor project to interactively visualize every step of the differential analysis, without programming. The application provides a rich and interactive web based graphical user interface built on R's shiny infrastructure. DEBrowser allows users to visualize data with various types of graphs that can be explored further by selecting and re-plotting any desired subset of data. Using the visualization approaches provided, users can determine and correct technical variations such as batch effects and sequencing depth that affect differential analysis. We show DEBrowser's ease of use by reproducing the analysis of two previously published data sets.

CONCLUSIONS: DEBrowser is a flexible, intuitive, web-based analysis platform that enables an iterative and interactive analysis of count data without any requirement of programming knowledge.

Keywords

Data visualization, Differential expression, Interactive data analysis, UMCCTS funding

Rights and Permissions

© The Author(s). 2019. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

DOI of Published Version

10.1186/s12864-018-5362-x

Source

BMC Genomics. 2019 Jan 5;20(1):6. doi: 10.1186/s12864-018-5362-x. Link to article on publisher's site

Journal/Book/Conference Title

BMC genomics

Related Resources

Link to Article in PubMed

PubMed ID

30611200

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

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