Recent technological evolutions have led to an exponential increase in data in all the omics fields. It is expected that integration of these different data sources, will drastically enhance our knowledge of the biological mechanisms behind genomic diseases such as cancer. However, the integration of different omics data still remains a challenge. In this work we propose an intuitive workflow for the integrative analysis of expression, mutation and copy number data taken from the METABRIC study on breast cancer. First, we present evidence that the expression profile of many important breast cancer genes consists of two modes or 'regimes', which contain important clinical information. Then, we show how the co-occurrence of these expression regimes can be used as an association measure between genes and validate our findings on the TCGA-BRCA study. Finally, we demonstrate how these co-occurrence measures can also be applied to link expression regimes to genomic aberrations, providing a more complete, integrative view on breast cancer. As a case study, an integrative analysis of the identified MLPH-FOXA1 association is performed, illustrating that the obtained expression associations are intimately linked to the underlying genomic changes. REVIEWERS: This article was reviewed by Dirk Walther, Francisco Garcia and Isabel Nepomuceno.

中文翻译：

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使用共现度量关联表达和基因组数据。

最近的技术发展导致所有组学领域的数据呈指数增长。预计这些不同数据源的集成将大大增强我们对基因组疾病（例如癌症）背后生物学机制的认识。但是，集成不同的组学数据仍然是一个挑战。在这项工作中，我们提出了一种直观的工作流程，用于对来自METABRIC乳腺癌研究的表达，突变和拷贝数数据进行综合分析。首先，我们提供证据表明许多重要的乳腺癌基因的表达谱由两种模式或“制度”组成，其中包含重要的临床信息。然后，我们展示了这些表达方式的共存如何可以用作基因之间的关联度量，并验证了我们在TCGA-BRCA研究中的发现。最后，我们证明了这些共现措施也可以用于将表达方案与基因组畸变联系起来，从而提供关于乳腺癌的更完整，综合的观点。作为案例研究，对鉴定出的MLPH-FOXA1关联进行了综合分析，表明所获得的表达关联与潜在的基因组变化密切相关。评论者：本文由Dirk Walther，Francisco Garcia和Isabel Nepomuceno进行了评论。作为案例研究，对鉴定出的MLPH-FOXA1关联进行了综合分析，表明所获得的表达关联与潜在的基因组变化密切相关。评论者：本文由Dirk Walther，Francisco Garcia和Isabel Nepomuceno进行了评论。作为案例研究，对鉴定出的MLPH-FOXA1关联进行了综合分析，表明所获得的表达关联与潜在的基因组变化密切相关。评论者：Dirk Walther，Francisco Garcia和Isabel Nepomuceno对本文进行了评论。