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利用跨HLA等位基因/超型的信息可改善表位预测。

Leveraging information across HLA alleles/supertypes improves epitope prediction.

作者信息

Heckerman David, Kadie Carl, Listgarten Jennifer

机构信息

Microsoft Research, Redmond, WA 98052, USA.

出版信息

J Comput Biol. 2007 Jul-Aug;14(6):736-46. doi: 10.1089/cmb.2007.R013.

Abstract

We present a model for predicting HLA class I restricted CTL epitopes. In contrast to almost all other work in this area, we train a single model on epitopes from all HLA alleles and supertypes, yet retain the ability to make epitope predictions for specific HLA alleles. We are therefore able to leverage data across all HLA alleles and/or their supertypes, automatically learning what information should be shared and also how to combine allele-specific, supertype-specific, and global information in a principled way. We show that this leveraging can improve prediction of epitopes having HLA alleles with known supertypes, and dramatically increases our ability to predict epitopes having alleles which do not fall into any of the known supertypes. Our model, which is based on logistic regression, is simple to implement and understand, is solved by finding a single global maximum, and is more accurate (to our knowledge) than any other model.

摘要

我们提出了一种预测HLA I类限制性CTL表位的模型。与该领域几乎所有其他工作不同的是,我们在来自所有HLA等位基因和超型的表位上训练单一模型,但仍保留对特定HLA等位基因进行表位预测的能力。因此,我们能够利用所有HLA等位基因和/或其超型的数据,自动学习应共享哪些信息,以及如何以有原则的方式组合等位基因特异性、超型特异性和全局信息。我们表明,这种利用可以改善对具有已知超型的HLA等位基因的表位预测,并显著提高我们预测具有不属于任何已知超型的等位基因的表位的能力。我们基于逻辑回归的模型易于实现和理解,通过找到单个全局最大值来求解,并且(据我们所知)比任何其他模型都更准确。

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