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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >Dynamic integration of gene annotation and its application to microarray analysis
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Dynamic integration of gene annotation and its application to microarray analysis

机译：基因注释的动态整合及其在微阵列分析中的应用

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摘要

Comprehensive and structured annotations for all genes on a microarray chip are essential for the interpretation of its expression data. Currently, most chip gene annotations are one-line free text descriptions that are often partial, outdated and unsuitable for large-scale data analysis. Therefore the interpretation of microarray gene expression clusters is often limited. Although researchers can manually navigate a collection of databases for better annotations, it is only practical for limited number of genes. Existing meta-databases fail to provide comprehensive categorized annotations for hundreds of genes simultaneously. We have developed an automatic system to address this issue. GeneView system monitors various data sources, extracts gene information from a source whenever it is updated, comprehensively matches genes, and integrates them into a central database by categories, such as pathway, genetic mapping, phenotype, expression profile, domain structure, protein interaction, disease association, and references. The system consists of four major components: (1) relational database; (2) data processing; (3) user curation; (4) data query. We evaluated it by analyzing genes on cDNA and Affymetrix Oligo chips. In both cases, the system provided more accurate and comprehensive information than those provided by the vendors or the chip users, and helped identify new common functions among genes in the same expression clusters.
机译：微阵列芯片上所有基因的全面和结构化注释对于解释其表达数据至关重要。当前，大多数芯片基因注释是单行的自由文本描述，这些描述通常是不完整的，过时的并且不适合大规模数据分析。因此，微阵列基因表达簇的解释常常受到限制。尽管研究人员可以手动导航数据库集合以获得更好的注释，但这仅适用于有限数量的基因。现有的元数据库无法同时为数百个基因提供全面的分类注释。我们开发了一个自动系统来解决此问题。 GeneView系统监视各种数据源，在更新时从源中提取基因信息，全面匹配基因，然后按类别将它们整合到中央数据库中，例如途径，遗传图谱，表型，表达谱，结构域，蛋白质相互作用，疾病协会和参考。该系统由四个主要部分组成：（1）关系数据库; （2）数据处理; （3）用户策展; （4）数据查询。我们通过分析cDNA和Affymetrix Oligo芯片上的基因来评估它。在这两种情况下，该系统提供的信息都比供应商或芯片用户提供的信息更为准确和全面，并有助于识别同一表达簇中基因之间的新共有功能。

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