Partial correlation analysis indicates causal relationships between GC-content, ezon density and recombination rate variation in the human genome

摘要：

Background: Several features are known to correlate with the GC-content in the human genome, including recombination rate, gene density and distance to telomere. However, by testing for pairwise correlation only, it is impossible to distinguish direct associations from indirect ones and to distinguish between causes and effects.Results: We use partial correlations to construct partially directed graphs for the following four variables: GC-content, recombination rate, exon density and distance-to-telomere. Recombination rate and exon density are unconditionally uncorrelated, but become inversely correlated by conditioning on GC-content. This pattern indicates a model where recombination rate and exon density are two independent causes of GC-content variation.Conclusions: Causal inference and graphical models are useful methods to understand genome evolution and the mechanisms of isochore evolution in the human genome.

作者: Jan Freudenberg Mingyi Wang Yaning Yang Wentian Li

作者单位: The Robert S Boas Center for Genomics and Human GeneticsFeinstein Institute for Medical Research, No Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA Department of Statistics and Finance, University of Science and Technology of China, Anhui 230026, H

会议类型: 国际会议

会议名称: The 7th Asia-Pacific Bioinformatics Conference(第七届亚太生物信息学大会)

会议地点: 北京

会议语种:英文

页码: 801-810

在线出版日期: 2009-01-01（万方平台首次上网日期，不代表论文的发表时间）