New strategy for the representation and the integration of biomolecular knowledge at a cellular scale
New strategy for the representation and the integration of biomolecular knowledge at a cellular scale
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DOI：
10.1093/nar/gkh681
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
de Daruvar, A
中科院分区：
文献类型：
--
作者：
Barriot, R;Poix, J;de Daruvar, A
测序和后测序实验方法的结合产生了大量的数据集合，这些数据在结构和语义上都高度异构。我们提出了一种整合此类数据的新策略。该策略使用结构化的序列集作为生物信息的统一表示，并定义了序列集之间相似性的概率度量。集合可以由已知具有生物学关系的序列（例如参与复合物或途径的蛋白质）或共享特定属性的相似值（例如表达谱）的序列组成。我们开发了一个软件 BlastSets，它实现了这一策略。它利用一个数据库，可以使用标准 XML 格式存储源自不同生物信息的集合。对于给定的查询集，BlastSets 返回在数据库中找到的与查询的相似性具有统计显着性的目标集。该工具使我们能够使用酿酒酵母的公开数据自动识别相关表达谱和生物途径之间经过验证的关系。它还用于基于表达谱的挖掘来检索复合体（核糖体）的成员。这些初步结果验证了该策略的相关性，并展示了 BlastSet 的巨大潜力。
The combination of sequencing and post-sequencing experimental approaches produces huge collections of data that are highly heterogeneous both in structure and in semantics. We propose a new strategy for the integration of such data. This strategy uses structured sets of sequences as a unified representation of biological information and defines a probabilistic measure of similarity between the sets. Sets can be composed of sequences that are known to have a biological relationship (e.g. proteins involved in a complex or a pathway) or that share similar values for a particular attribute (e.g. expression profile). We have developed a software, BlastSets, which implements this strategy. It exploits a database where the sets derived from diverse biological information can be deposited using a standard XML format. For a given query set, BlastSets returns target sets found in the database whose similarity to the query is statistically significant. The tool allowed us to automatically identify verified relationships between correlated expression profiles and biological pathways using publicly available data for Saccharomyces cerevisiae. It was also used to retrieve the members of a complex (ribosome) based on the mining of expression profiles. These first results validate the relevance of the strategy and demonstrate the promising potential of BlastSets.