期刊
BIOINFORMATICS
卷 24, 期 9, 页码 1161-1167出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btn096
关键词
-
类别
资金
- NIAID NIH HHS [P30 AI051519, R01 AI060496, 5 P30 AI051519] Funding Source: Medline
- NICHD NIH HHS [R01 HD044078] Funding Source: Medline
- NIGMS NIH HHS [T32 GM007288, GM007288] Funding Source: Medline
- PHS HHS [HSN26620-0400054C] Funding Source: Medline
Motivation: Representations of the genome can be generated by the selection of a subpopulation of restriction fragments using ligation-mediated PCR. Such representations form the basis for a number of high-throughput assays, including the HELP assay to study cytosine methylation. We find that HELP data analysis is complicated not only by PCR amplification heterogeneity but also by a complex and variable distribution of cytosine methylation. To address this, we created an analytical pipeline and novel normalization approach that improves concordance between microarray-derived data and single locus validation results, demonstrating the value of the analytical approach. A major influence on the PCR amplification is the size of the restriction fragment, requiring a quantile normalization approach that reduces the influence of fragment length on signal intensity. Here we describe all of the components of the pipeline, which can also be applied to data derived from other assays based on genomic representations. Contact: jgreally@aecom.yu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据