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Biclustering for the comprehensive search of correlated gene expression patterns using clustered seed expansion

机译:利用簇状种子扩展对相关基因表达模式进行全面检索

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Background In a functional analysis of gene expression data, biclustering method can give crucial information by showing correlated gene expression patterns under a subset of conditions. However, conventional biclustering algorithms still have some limitations to show comprehensive and stable outputs. Results We propose a novel biclustering approach called “BIclustering by Correlated and Large number of Individual Clustered seeds (BICLIC)” to find comprehensive sets of correlated expression patterns in biclusters using clustered seeds and their expansion with correlation of gene expression. BICLIC outperformed competing biclustering algorithms by completely recovering implanted biclusters in simulated datasets with various types of correlated patterns: shifting, scaling, and shifting-scaling. Furthermore, in a real yeast microarray dataset and a lung cancer microarray dataset, BICLIC found more comprehensive sets of biclusters that are significantly enriched to more diverse sets of biological terms than those of other competing biclustering algorithms. Conclusions BICLIC provides significant benefits in finding comprehensive sets of correlated patterns and their functional implications from a gene expression dataset.
机译:背景技术在基因表达数据的功能分析中,双聚类分析法可以通过显示条件子集下的相关基因表达模式来提供关键信息。但是,常规的双簇算法仍存在一些局限性,无法显示全面而稳定的输出。结果我们提出了一种新颖的双聚类方法,称为“通过相关且大量的单个聚类种子进行双聚类(BICLIC)”,以使用聚类种子在双聚类中找到全面的相关表达模式集,并扩展它们与基因表达的相关性。 BICLIC通过完全恢复具有各种相关模式类型的模拟数据集中的已植入双簇,从而优于竞争双簇算法,这些相关模式包括移位,缩放和移位缩放。此外,在真实的酵母微阵列数据集和肺癌微阵列数据集中,BICLIC发现了比其他竞争性双聚类算法更全面的双聚类集,这些双聚类集显着丰富了更多的生物术语集。结论BICLIC在从基因表达数据集中找到全面的相关模式集及其功能含义方面具有显着优势。

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