title: A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics.
abstract: 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.
authors: Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America.
authors: Qiang
authors: Q
authors: Song
authors: Benjamin
authors: B
authors: Decato
authors: Elizabeth E
authors: EE
authors: Hong
authors: Meng
authors: M
authors: Zhou
authors: Fang
authors: F
authors: Fang
authors: Jianghan
authors: J
authors: Qu
authors: Tyler
authors: T
authors: Garvin
authors: Michael
authors: M
authors: Kessler
authors: Jun
authors: J
authors: Zhou
authors: Andrew D
authors: AD
authors: Smith
mesh_terms: D000818:Animals; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D016208:Databases, Factual; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism*; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D002679:Pan troglodytes / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D009363:Neoplasm Proteins; D004247:DNA