Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes
Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes
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DOI：
10.1016/j.gene.2005.09.040
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发表时间：
2006-01-03
期刊：
影响因子：
3.5
通讯作者：
Ikemura, T
中科院分区：
文献类型：
--
作者：
Abe, T;Sugawara, H;Ikemura, T
需要新的工具来全面比较目前可用的大量基因组序列的种间特征。自组织映射（SOM）是一种无监督的神经网络算法，它是一种有效的工具，用于在单个映射上对高维复杂数据进行聚类和可视化。在批学习SOM的基础上，对传统的SOM进行了改进，使学习过程和生成的图与数据输入的顺序无关。我们产生的SOM的三和四核苷酸频率在10-和100-kb的序列片段，从38个真核生物，几乎完整的基因组序列。SOM识别基因组序列中的物种特异性特征（寡核苷酸频率的关键组合），允许对序列进行物种特异性分类，而无需任何关于物种的信息。我们还生成了SOM的四核苷酸频率在1-kb的序列片段从人类基因组中，发现序列的四个功能类别（5'和3' UTR，CDS和内含子）主要根据类别进行分类。由于SOM具有很高的分类能力和可视化能力，因此它是一种高效、有效的基因组信息提取工具。(C)2005 Elsevier B. V.保留所有权利。
Novel tools are needed for comprehensive comparisons of interspecies characteristics of massive amounts of genomic sequences currently available. An unsupervised neural network algorithm, Self-Organizing Map (SOM), is an effective tool for clustering and visualizing high-dimensional complex data on a single map. We modified the conventional SOM, oil the basis of batch-learning SOM, for genome informatics making the learning process and resulting map independent of the order of data input. We generated the SOMs for tri- and tetranucleotide frequencies in 10- and 100-kb sequence fragments from 38 eukaryotes for which almost complete genome sequences are available. SOM recognized species-specific characteristics (key combinations of oligonucleotide frequencies) in the genomic sequences, permitting species-specific classification of the sequences without any information regarding the species. We also generated the SOM for tetranucleotide frequencies in 1-kb sequence fragments from the human genome and found sequences for four functional categories (5' and 3' UTRs, CDSs and introns) were classified primarily according to the categories. Because the classification and visualization power is very high, SOM is an efficient and powerful tool for extracting a wide range of genome information. (C) 2005 Elsevier B.V. All rights reserved.