A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics

• Published in: PloS one Vol. 8; no. 12; p. e81148
• Main Authors: Song, Qiang, Decato, Benjamin, Hong, Elizabeth E, Zhou, Meng, Fang, Fang, Qu, Jianghan, Garvin, Tyler, Kessler, Michael, Zhou, Jun, Smith, Andrew D
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 06.12.2013; Public Library of Science (PLoS)
• Subjects: Animals; Binding sites; Biological evolution; Biology; Bisulfite; Comparative analysis; Databases, Factual; Datasets; Deoxyribonucleic acid; DNA; DNA - genetics; DNA - metabolism; DNA Methylation; DNA sequencing; Epigenesis, Genetic; Epigenetics; Epigenomics - methods; Eukaryotes; Feature extraction; Gene expression; Gene sequencing; Genome; Genomes; Genomics; High-Throughput Nucleotide Sequencing; Humans; Metadata; Methylation; Mitochondrial DNA; Neoplasm Proteins - genetics; Neoplasm Proteins - metabolism; Neoplasms - genetics; Neoplasms - metabolism; Neoplasms - pathology; Open source software; Pan troglodytes - genetics; Pipelines; Public domain; Researchers; Sequence Analysis, DNA; Stem cells; Studies; Sulfites; Transcription factors; Los Angeles California; United States > US; California
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0081148

DNA methylation is implicated in a surprising diversity of regulatory, evolutionary processes and diseases in eukaryotes. The introduction of whole-genome bisulfite sequencing has enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness of methylome data in understanding a variety of genomic phenomena. As the number of publicly available whole-genome bisulfite sequencing studies reaches into the hundreds, reliable and convenient tools for comparing and analyzing methylomes become increasingly important. We present MethPipe, a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.