BioCompass: A Novel Functional Inference Tool that Utilizes MeSH Hierarchy to Analyze Groups of Genes
BioCompass: A Novel Functional Inference Tool that Utilizes MeSH Hierarchy to Analyze Groups of Genes
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发表时间：
2008
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通讯作者：
Takeru Nakazato;Toru Takinaka;H. Mizuguchi;H. Matsuda;H. Bono;M. Asogawa
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作者：
Takeru Nakazato;Toru Takinaka;H. Mizuguchi;H. Matsuda;H. Bono;M. Asogawa
微阵列技术已被广泛应用于生物学研究人员，以识别与疾病和药物等条件相关的基因。迄今为止，已经开发了许多方法来分析涵盖大量基因的数据，但它们只关注统计显著性，而不能用生物学概念解读数据。利用基因本体（Gene Ontology， GO）对数据进行生物学解释；然而，它仅限于特定的本体，如生物过程、分子功能、细胞成分等。在这里，我们尝试应用MeSH（医学主题标题）从生物学的角度来解释基因组。为了将MeSH术语分配给基因，在本研究中，使用机器学习从MEDLINE的全部数据中检索与基因相关的上下文，然后从检索到的文章中提取MeSH术语。利用开发的方法，我们实现了一个名为“生物指南针”的软件。利用MeSH和GO树生成与基因组相关的疾病MeSH术语高分列表和分层列表，并通过文章中提取的关联关系将基因连接起来，绘制出接线图。研究人员可以很容易地检索与基因组相关的基因和感兴趣的关键词，例如疾病和药物。利用检索到的MeSH术语和OMIM结合，我们可以获得更多与靶基因相关的疾病信息。生物罗盘帮助研究人员从生物学的角度解释基因群，如微阵列数据。
Microarray technology has become employed widely for biological researchers to identify genes associated with conditions such as diseases and drugs. To date, many methods have been developed to analyze data covering a large number of genes, but they focus only on statistical significance and cannot decipher the data with biological concepts. Gene Ontology (GO) is utilized to understand the data with biological interpretation; however, it is restricted to specific ontology such as biological process, molecular function, and cellular component. Here, we attempted to apply MeSH (Medical Subject Headings) to interpret groups of genes from biological viewpoint. To assign MeSH terms to genes, in this study, contexts associated with genes are retrieved from full set of MEDLINE data using machine learning, and then extracted MeSH terms from retrieved articles. Utilizing the developed method, we implemented a software called BioCompass. It generates high-scoring lists and hierarchical lists for diseases MeSH terms associated with groups of genes to utilize MeSH and GO tree, and illustrated a wiring diagram by linking genes with extracted association from articles. Researchers can easily retrieve genes and keywords of interest, such as diseases and drugs, associated with groups of genes. Using retrieved MeSH terms and OMIM in conjunction with, we could obtain more disease information associated with target gene. BioCompass helps researchers to interpret groups of genes such as microarray data from a biological viewpoint.