Sapienza University of Rome, Rome 00185, Italy.
Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Turin 10126, Italy.
Gigascience. 2022 Dec 28;12. doi: 10.1093/gigascience/giad010. Epub 2023 Feb 28.
Biological networks are often used to describe the relationships between relevant entities, particularly genes and proteins, and are a powerful tool for functional genomics. Many important biological problems can be investigated by comparing biological networks between different conditions or networks obtained with different techniques.
We show that contrast subgraphs, a recently introduced technique to identify the most important structural differences between 2 networks, provide a versatile tool for comparing gene and protein networks of diverse origin. We demonstrate the use of contrast subgraphs in the comparison of coexpression networks derived from different subtypes of breast cancer, coexpression networks derived from transcriptomic and proteomic data, and protein-protein interaction networks assayed in different cell lines.
These examples demonstrate how contrast subgraphs can provide new insight in functional genomics by extracting the gene/protein modules whose connectivity is most altered between 2 conditions or experimental techniques.
生物网络常用于描述相关实体（特别是基因和蛋白质）之间的关系，是功能基因组学的有力工具。通过比较不同条件下的生物网络或使用不同技术获得的网络，许多重要的生物学问题都可以得到研究。
我们表明，对比子图是一种最近引入的技术，用于识别两个网络之间最重要的结构差异，可以为比较不同来源的基因和蛋白质网络提供一种通用的工具。我们展示了对比子图在比较不同乳腺癌亚型的共表达网络、基于转录组和蛋白质组数据的共表达网络以及在不同细胞系中检测到的蛋白质-蛋白质相互作用网络方面的应用。
这些例子表明，对比子图如何通过提取两个条件或实验技术之间连接性变化最大的基因/蛋白质模块，为功能基因组学提供新的见解。
