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Discovery of error-tolerant biclusters from noisy gene expression data

机译:从嘈杂的基因表达数据中发现容错双聚簇

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摘要

BackgroundAn important analysis performed on microarray gene-expression data is to discover biclusters, which denote groups of genes that are coherently expressed for a subset of conditions. Various biclustering algorithms have been proposed to find different types of biclusters from these real-valued gene-expression data sets. However, these algorithms suffer from several limitations such as inability to explicitly handle errorsoise in the data; difficulty in discovering small bicliusters due to their top-down approach; inability of some of the approaches to find overlapping biclusters, which is crucial as many genes participate in multiple biological processes. Association pattern mining also produce biclusters as their result and can naturally address some of these limitations. However, traditional association mining only finds exact biclusters, which limits its applicability in real-life data sets where the biclusters may be fragmented due to random noise/errors. Moreover, as they only work with binary or boolean attributes, their application on gene-expression data require transforming real-valued attributes to binary attributes, which often results in loss of information. Many past approaches have tried to address the issue of noise and handling real-valued attributes independently but there is no systematic approach that addresses both of these issues together.
机译:背景技术对微阵列基因表达数据进行的一项重要分析是发现双链体,双链体表示在一组条件下连贯表达的基因组。为了从这些实值基因表达数据集中找到不同类型的双聚类,已经提出了各种双聚类算法。但是,这些算法存在一些局限性,例如无法显式处理数据中的错误/噪声。由于采用自上而下的方法,很难发现小型biclister;一些方法无法找到重叠的二聚体,这是至关重要的,因为许多基因参与了多个生物过程。关联模式挖掘也产生了bicluster,结果自然可以解决其中的一些限制。但是,传统的关联挖掘仅能找到精确的双峰,这限制了它在现实数据集中的适用性,在这些数据中,双峰可能会由于随机噪声/错误而破碎。此外,由于它们仅使用二进制或布尔属性,因此它们在基因表达数据上的应用需要将实值属性转换为二进制属性,这通常会导致信息丢失。过去的许多方法都试图解决噪声问题并独立处理实值属性,但是没有系统的方法可以同时解决这两个问题。

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