Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

被引：82

作者：

Kolbe, D

Taylor, J

Elnitski, L

Eswara, P

Li, J

Miller, W

Hardison, R

Chiaromonte, F ^{[1
]}

机构：

[1] Penn State Univ, Dept Stat, University Pk, PA 16802 USA

[2] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA

[3] Penn State Univ, Dept Biol, University Pk, PA 16802 USA

[4] Penn State Univ, Dept Comp Sci & Engn, University Pk, PA 16802 USA

[5] Penn State Univ, Dept Hlth Evaluat Sci, University Pk, PA 16802 USA

[6] Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA

来源：

GENOME RESEARCH | 2004年 / 14卷 / 04期

关键词：

D O I：

10.1101/gr.1976004

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We generalize the computation of the Regulatory Potential (RP) score from two-way alignments of human and mouse to three-way alignments of human, mouse, and rat. This requires overcoming technical challenges that arise because the complexity of the models underlying the score increases exponentially with the number of species. Despite the close evolutionary proximity of rat to mouse, we find that adding the rat sequence increases our ability to predict genomic sites that regulate gene transcription. A variant of the RP scoring scheme that accounts for local variation in neutral mutational patterns further improves our predictions.

引用

页码：700 / 707

页数：8

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