An improved scoring scheme for predicting glycan structures from gene expression data.
An improved scoring scheme for predicting glycan structures from gene expression data.
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DOI：
10.11234/gi1990.18.237
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发表时间：
2007
期刊：
影响因子：
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通讯作者：
Akitsugu Suga;Yoshihiro Yamanishi;K. Hashimoto;S. Goto;M. Kanehisa
中科院分区：
文献类型：
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作者：
Akitsugu Suga;Yoshihiro Yamanishi;K. Hashimoto;S. Goto;M. Kanehisa
从糖基转移酶（glycosyltransferases，GT）的基因表达预测聚糖结构是计算生物学中一个具有挑战性的新领域，因为聚糖链的生物合成是在GT表达的控制下进行的。在本文中，我们开发了一种新的方法来预测聚糖结构的基因表达数据。所提出的方法有两个主要的原始方面。首先，我们提出通过从全局聚糖结构图中估计缺失的聚糖来增加可预测聚糖结构候选物的数量，这使我们能够预测未存储在数据库中的新聚糖结构。其次，我们提出了一个更一般的评分方案的基础上实值基因表达强度，而不是将其转换为二进制信息。在结果中，我们应用所提出的方法来预测癌症特异性聚糖结构从急性淋巴细胞白血病（ALL）和急性髓细胞白血病（AML）患者的基因表达谱。我们证实，根据文献，几种预测的聚糖结构成功地对应于已知的癌症特异性聚糖结构，并且我们的方法在统计学显著水平上优于以前的方法。
The prediction of glycan structures from gene expression of glycosyltransferases (GTs) is a challenging new area in computational biology because the biosynthesis of glycan chains is under the control of GT expression. In this paper we developed a new method for predicting glycan structures from gene expression data. There are two main original aspects of the proposed method. First, we proposed to increase the number of predictable glycan structure candidates by estimating missing glycans from a global glycan structure map, which enables us to predict new glycan structures that are not stored in the database. Second, we proposed a more general scoring scheme based on real-valued gene expression intensity rather than converting it into binary information. In the result we applied the proposed method to predicting cancer-specific glycan structures from gene expression profiles for patients of acute lymphocytic leukemia (ALL) and acute myelocytic leukemia (AML). We confirmed that several of the predicted glycan structures successfully correspond to known cancer-specific glycan structures according to the literature, and our method outperforms the previous methods at a statistically significant level.