title: CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers.
abstract: BACKGROUND
  DNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. Also, experimental and computational technologies make it possible to find the functional relationship between cancer-specific methylation patterns and their clinicopathological parameters.
  
  
  RESULTS
  Cancer methylome system (CMS) is a web-based database application designed for the visualization, comparison and statistical analysis of human cancer-specific DNA methylation. Methylation intensities were obtained from MBDCap-sequencing, pre-processed and stored in the database. 191 patient samples (169 tumor and 22 normal specimen) and 41 breast cancer cell-lines are deposited in the database, comprising about 6.6 billion uniquely mapped sequence reads. This provides comprehensive and genome-wide epigenetic portraits of human breast cancer and endometrial cancer to date. Two views are proposed for users to better understand methylation structure at the genomic level or systemic methylation alteration at the gene level. In addition, a variety of annotation tracks are provided to cover genomic information. CMS includes important analytic functions for interpretation of methylation data, such as the detection of differentially methylated regions, statistical calculation of global methylation intensities, multiple gene sets of biologically significant categories, interactivity with UCSC via custom-track data. We also present examples of discoveries utilizing the framework.
  
  
  CONCLUSIONS
  CMS provides visualization and analytic functions for cancer methylome datasets. A comprehensive collection of datasets, a variety of embedded analytic functions and extensive applications with biological and translational significance make this system powerful and unique in cancer methylation research. CMS is freely accessible at: http://cbbiweb.uthscsa.edu/KMethylomes/.
authors: Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America.
authors: Fei
authors: F
authors: Gu
authors: Mark S
authors: MS
authors: Doderer
authors: Yi-Wen
authors: YW
authors: Huang
authors: Juan C
authors: JC
authors: Roa
authors: Paul J
authors: PJ
authors: Goodfellow
authors: E Lynette
authors: EL
authors: Kizer
authors: Tim H M
authors: TH
authors: Huang
authors: Yidong
authors: Y
authors: Chen
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D019175:DNA Methylation; D030541:Databases, Genetic; D016889:Endometrial Neoplasms / Q000235:genetics*; D005260:Female; D052138:Genes, Neoplasm; D015894:Genome, Human; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D011401:Promoter Regions, Genetic; D014584:User-Computer Interface
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