Prediction of glycan structures from gene expression data based on glycosyltransferase reactions
Prediction of glycan structures from gene expression data based on glycosyltransferase reactions
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DOI：
10.1093/bioinformatics/bti666
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发表时间：
2005-11-01
期刊：
影响因子：
5.8
通讯作者：
Kanehisa, M
中科院分区：
文献类型：
--
作者：
Kawano, S;Hashimoto, K;Kanehisa, M
研究动机：聚糖链是由几种糖基转移酶（GT）合成的。因此，一旦我们知道了基因组、转录组或蛋白质组中GT的所有组成部分，原则上就可以预测生物体或细胞特定阶段中可能的聚糖结构的所有组成部分。在这里，我们表明，可以预测从一组GT的转录组中的聚糖结构的剧目。也就是说，使用知识的聚糖结构的特点，我们可以预测聚糖的结构，从不完整的或嘈杂的数据，如DNA微阵列data.Results：首先，我们构建了一个反应模式库，包括键形成模式的GT反应，并调查了所有的反应模式在聚糖数据库中的共现频率。随后使用该文库和共现评分预测聚糖结构。在预测方法中还实施了罚分。然后，我们检查了预测的性能，通过留一交叉验证方法使用KEGG GLYCAN数据库中的个体反应模式配置文件作为虚拟表达配置文件。预测准确率为81%。最后，我们将预测方法应用于真实的表达数据。利用人癌细胞表达谱预测了含有唾液酸和唾液酸刘易斯X抗原表位的糖链结构，与实验结果吻合较好。
Motivation: Glycan chains are synthesized by a combination of several kinds of glycosyltransferases (GTs). Thus, once we know the repertoire of GTs in the genome, in the transcriptome or in the proteome, it should in principle be possible to predict the repertoire of possible glycan structures in an organism or at a specific stage of the cell. Here, we show that a repertoire of glycan structures can be predicted from the set of GTs in the transcriptome. That is, using knowledge about glycan structure characteristics, we can predict glycan structures from incomplete or noisy data such as DNA microarray data.Results: First, we constructed a reaction pattern library consisting of bond-formation patterns of GT reactions and investigated the co-occurrence frequencies of all reaction patterns in the glycan database. This was followed by the prediction of glycan structures using this library and a co-occurrence score. A penalty score was also implemented in the prediction method. Then we examined the performance of prediction by the leave-one-out cross validation method using individual reaction pattern profiles in the KEGG GLYCAN database as virtual expression profiles. The accuracy of prediction was 81%. Finally, we applied the prediction method to real expression data. Using expression profiles from the human carcinoma cell, glycan structures with sialic acid and sialyl Lewis X epitope were predicted, which corresponded well with experimental results.