title: BioVLAB-mCpG-SNP-EXPRESS: A system for multi-level and multi-perspective analysis and exploration of DNA methylation, sequence variation (SNPs), and gene expression from multi-omics data.
abstract: Measuring gene expression, DNA sequence variation, and DNA methylation status is routinely done using high throughput sequencing technologies. To analyze such multi-omics data and explore relationships, reliable bioinformatics systems are much needed. Existing systems are either for exploring curated data or for processing omics data in the form of a library such as R. Thus scientists have much difficulty in investigating relationships among gene expression, DNA sequence variation, and DNA methylation using multi-omics data. In this study, we report a system called BioVLAB-mCpG-SNP-EXPRESS for the integrated analysis of DNA methylation, sequence variation (SNPs), and gene expression for distinguishing cellular phenotypes at the pairwise and multiple phenotype levels. The system can be deployed on either the Amazon cloud or a publicly available high-performance computing node, and the data analysis and exploration of the analysis result can be conveniently done using a web-based interface. In order to alleviate analysis complexity, all the process are fully automated, and graphical workflow system is integrated to represent real-time analysis progression. The BioVLAB-mCpG-SNP-EXPRESS system works in three stages. First, it processes and analyzes multi-omics data as input in the form of the raw data, i.e., FastQ files. Second, various integrated analyses such as methylation vs. gene expression and mutation vs. methylation are performed. Finally, the analysis result can be explored in a number of ways through a web interface for the multi-level, multi-perspective exploration. Multi-level interpretation can be done by either gene, gene set, pathway or network level and multi-perspective exploration can be explored from either gene expression, DNA methylation, sequence variation, or their relationship perspective. The utility of the system is demonstrated by performing analysis of phenotypically distinct 30 breast cancer cell line data set. BioVLAB-mCpG-SNP-EXPRESS is available at http://biohealth.snu.ac.kr/software/biovlab_mcpg_snp_express/.
authors.affiliation: School of Informatics and Computing, Indiana University Bloomington, IN 47405, USA.
authors.forename: Heejoon
authors.initials: H
authors.lastname: Chae
authors.affiliation: Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea.
authors.forename: Sangseon
authors.initials: S
authors.lastname: Lee
authors.affiliation: Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea.
authors.forename: Seokjun
authors.initials: S
authors.lastname: Seo
authors.affiliation: Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea.
authors.forename: Daekyoung
authors.initials: D
authors.lastname: Jung
authors.affiliation: Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.
authors.forename: Hyeonsook
authors.initials: H
authors.lastname: Chang
authors.affiliation: Indiana University School of Medicine, Department of Cellular and Integrative Physiology, Medical Sciences Program, USA.
authors.forename: Kenneth P
authors.initials: KP
authors.lastname: Nephew
authors.affiliation: Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea; Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. Electronic address: sunkim.bioinfo@snu.ac.kr.
authors.forename: Sun
authors.initials: S
authors.lastname: Kim
mesh_terms: D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation / Q000235:genetics; D030541:Databases, Genetic; D014644:Genetic Variation; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012984:Software
keywords: DNA methylation; Gene expression; Integrated analysis; SNP