Extraction of species-specific glycan substructures.
Extraction of species-specific glycan substructures.
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DOI：
10.11234/gi1990.15.69
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发表时间：
2004
期刊：
影响因子：
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通讯作者：
Yoshiyuki Hizukuri;Yoshihiro Yamanishi;K. Hashimoto;M. Kanehisa
中科院分区：
文献类型：
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作者：
Yoshiyuki Hizukuri;Yoshihiro Yamanishi;K. Hashimoto;M. Kanehisa
多糖是附着在某些脂质或蛋白质上的碳水化合物糖链，具有丰富的结构，在细胞通讯、蛋白质相互作用和免疫中发挥着关键作用。KEGG/Glycan数据库中存储的一些多糖结构的可用性使我们有可能对多糖进行大规模的比较研究。在本文中，我们提出了一种新的方法来比较某些生物体的糖链结构并提取其特征的糖链亚结构。在该算法中，我们考虑了糖链合成和糖基转移酶的几个生物学方面，提出了一种新的糖链结构相似性度量，并在支持向量机的框架下对其分类能力进行了实验，验证了该相似性度量的有效性。最后，我们的方法成功地提取了一组分别具有人、大鼠、小鼠、牛、猪、鸡、酵母、小麦和梧桐树特有的亚结构。我们证实，我们的方法提取的特征亚结构对应于肾脏中被称为伽马-谷氨酰转肽酶物种特异性糖链的亚结构。
Glycans, which are carbohydrate sugar chains attached to some lipids or proteins, have a huge variety of structures and play a key role in cell communication, protein interaction and immunity. The availability of a number of glycan structures stored in the KEGG/GLYCAN database makes it possible for us to conduct a large-scale comparative research of glycans. In this paper, we present a novel approach to compare glycan structures and extract characteristic glycan substructures of certain organisms. In the algorithm we developed a new similarity measure of glycan structures taking into account of several biological aspects of glycan synthesis and glycosyltransferases, and we confirmed the validity of our similarity measure by conducting experiments on its ability to classify glycans between organisms in the framework of a support vector machine. Finally, our method successfully extracted a set of candidates of substructrues which are characteristic to human, rat, mouse, bovine, pig, chicken, yeast, wheat and sycamore, respectively. We confirmed that the characteristic substructures extracted by our method correspond to the substructures which are known as the species-specific sugar chain of gamma-glutamyltranspeptidases in the kidney.