Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns
Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns
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DOI：
10.1093/bioinformatics/18.5.725
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发表时间：
2002-05-01
期刊：
影响因子：
5.8
通讯作者：
Wong, LS
中科院分区：
文献类型：
--
作者：
Li, JY;Wong, LS
动机和结果：与疾病显著相关的基因组可以通过进行一系列基因表达实验来检测。这项工作旨在发现满足以下性质的特殊类型的基因组。在每个组中，发现其成员基因在一类细胞中以大频率一对一地包含在基因表达水平的预定区间中，但在另一类细胞中从未一致地发现在这些区间中。我们称这些基因组为新兴模式，以强调模式在两类细胞之间的频率变化。我们使用有效的离散化和基因选择方法，以获得最具歧视性的基因。我们还使用有效的算法来从这些基因中获得模式。根据我们对ALL/AML数据集和结肠肿瘤数据集的研究，一些由一个或多个基因组成的模式可以达到90%甚至100%的高频率。换句话说，它们几乎或完全支配一类细胞，即使它们很少出现在另一类细胞中。所发现的模式被用来分类新的细胞具有更高的准确性比其他报告的方法。基于这些模式，我们还推测了个性化治疗计划的可能性，该计划通过调节一些基因的表达水平将结肠肿瘤细胞转化为正常细胞。
Motivations and Results: Gene groups that are significantly related to a disease can be detected by conducting a series of gene expression experiments. This work is aimed at discovering special types of gene groups that satisfy the following property. In each group, its member genes are found to be one-to-one contained in pre-determined intervals of gene expression level with a large frequency in one class of cells but are never found unanimously in these intervals in the other class of cells. We call these gene groups emerging patterns, to emphasize the patterns' frequency changes between two classes of cells. We use effective discretization and gene selection methods to obtain the most discriminatory genes. We also use efficient algorithms to derive the patterns from these genes. According to our studies on the ALL/AML dataset and the colon tumor dataset, some patterns, which consist of one or more genes, can reach a high frequency of 90%, or even 100%. In other words, they nearly or fully dominate one class of cells, even though they rarely occur in the other class. The discovered patterns are used to classify new cells with a higher accuracy than other reported methods. Based on these patterns, we also conjecture the possibility of a personalized treatment plan which converts colon tumor cells into normal cells by modulating the expression levels of a few genes.