Theoretical and empirical quality assessment of transcription factor-binding motifs.
Theoretical and empirical quality assessment of transcription factor-binding motifs.
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DOI：
10.1093/nar/gkq710
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发表时间：
2011-02
影响因子：
14.9
通讯作者：
van Helden J
中科院分区：
文献类型：
--
作者：
Medina-Rivera A;Abreu-Goodger C;Thomas-Chollier M;Salgado H;Collado-Vides J;van Helden J
Position-specific scoring matrices (PSSMs) are routinely used to predict transcription factor (TF)-binding sites in genome sequences. However, their reliability to predict novel binding sites can be far from optimum, due to the use of a small number of training sites or the inappropriate choice of parameters when building the matrix or when scanning sequences with it. Measures of matrix quality such as E-value and information content rely on theoretical models, and may fail in the context of full genome sequences. We propose a method, implemented in the program ‘matrix-quality’, that combines theoretical and empirical score distributions to assess reliability of PSSMs for predicting TF-binding sites. We applied ‘matrix-quality’ to estimate the predictive capacity of matrices for bacterial, yeast and mouse TFs. The evaluation of matrices from RegulonDB revealed some poorly predictive motifs, and allowed us to quantify the improvements obtained by applying multi-genome motif discovery. Interestingly, the method reveals differences between global and specific regulators. It also highlights the enrichment of binding sites in sequence sets obtained from high-throughput ChIP-chip (bacterial and yeast TFs), and ChIP–seq and experiments (mouse TFs). The method presented here has many applications, including: selecting reliable motifs before scanning sequences; improving motif collections in TFs databases; evaluating motifs discovered using high-throughput data sets.
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影响因子：
3
作者：
Bailey TL;Bodén M;Whitington T;Machanick P
通讯作者：
Machanick P
影响因子：
5.6
作者：
SCHNEIDER, TD;STORMO, GD;EHRENFEUCHT, A
通讯作者：
EHRENFEUCHT, A
影响因子：
5.8
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Thijs, G;Lescot, M;Moreau, Y
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Moreau, Y
影响因子：
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Pepke, Shirley;Wold, Barbara;Mortazavi, Ali
通讯作者：
Mortazavi, Ali
影响因子：
5.8
作者：
Montgomery, SB;Griffith, OL;Jones, SJM
通讯作者：
Jones, SJM