Genome sequencing technology has generated a vast amount of genomic and epigenomic data, and has provided us a great opportunity to study gene functions on a global scale from an epigenomic view. In the last decade, network-based studies, such as those based on PPI networks and co-expression networks, have shown good performance in capturing functional relationships between genes. However, the functions of a gene and the mechanism of interaction of genes with each other to elucidate their functions are still not entirely clear. Here, we construct a gene co-opening network based on chromatin accessibility of genes. We show that genes related to a specific biological process or the same disease tend to be clustered in the co-opening network. This understanding allows us to detect functional clusters from the network and to predict new functions for genes. We further apply the network to prioritize disease genes for Psoriasis, and demonstrate the power of the joint analysis of the co-opening network and GWAS data in identifying disease genes. Taken together, the co-opening network provides a new viewpoint for the elucidation of gene associations and the interpretation of disease mechanisms.

中文翻译：

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基因共同开放网络破译基因功能关系

基因组测序技术已产生了大量的基因组和表观基因组数据，并为我们提供了一个从表观基因组的角度研究全球范围内基因功能的绝好机会。在过去的十年中，基于网络的研究（例如基于PPI网络和共表达网络的研究）显示出在捕获基因之间的功能关系方面的良好性能。然而，基因的功能以及基因相互阐明其功能的机制仍不完全清楚。在这里，我们基于基因的染色质可及性构建了一个基因共同开放网络。我们显示与特定的生物过程或相同的疾病有关的基因往往会聚集在共同开放的网络中。这种理解使我们能够从网络中检测功能簇，并预测基因的新功能。我们进一步应用该网络对疾病基因进行优先排序银屑病，并展示在鉴定疾病基因的共开口网络和GWAS数据的联合分析的功率。总之，共同开放网络为阐明基因关联和解释疾病机制提供了新观点。