Network-based identification of biomarkers for colon adenocarcinoma
Network-based identification of biomarkers for colon adenocarcinoma
复制标题
基于网络的结肠腺癌生物标志物鉴定
DOI：
10.1186/s12885-020-07157-w
复制
发表时间：
2020-07-17
期刊：
影响因子：
3.8
通讯作者：
Liu, Xiaoping
中科院分区：
文献类型：
--
作者：
Hu, Fuyan;Wang, Qing;Liu, Xiaoping
BackgroundAs one of the most common cancers with high mortality in the world, we are still facing a huge challenge in the prevention and treatment of colon cancer. With the rapid development of high throughput technologies, new biomarkers identification for colon cancer has been confronted with the new opportunities and challenges.MethodsWe firstly constructed functional networks for each sample of colon adenocarcinoma (COAD) by using a sample-specific network (SSN) method which can construct individual-specific networks based on gene expression profiles of a single sample. The functional genes and interactions were identified from the functional networks, respectively.ResultsClassification and subtyping were used to test the function of the functional genes and interactions. The results of classification showed that the functional genes could be used as diagnostic biomarkers. The subtypes displayed different mechanisms, which were shown by the functional and pathway enrichment analysis for the representative genes of each subtype. Besides, subtype-specific molecular patterns were also detected, such as subtype-specific clinical and mutation features. Finally, 12 functional genes and 13 functional edges could serve as prognosis biomarkers since they were associated with the survival rate of COAD.ConclusionsIn conclusion, the functional genes and interactions in the constructed functional network could be used as new biomarkers for COAD.
BackgroundAs one of the most common cancers with high mortality in the world, we are still facing a huge challenge in the prevention and treatment of colon cancer. With the rapid development of high throughput technologies, new biomarkers identification for colon cancer has been confronted with the new opportunities and challenges.MethodsWe firstly constructed functional networks for each sample of colon adenocarcinoma (COAD) by using a sample-specific network (SSN) method which can construct individual-specific networks based on gene expression profiles of a single sample. The functional genes and interactions were identified from the functional networks, respectively.ResultsClassification and subtyping were used to test the function of the functional genes and interactions. The results of classification showed that the functional genes could be used as diagnostic biomarkers. The subtypes displayed different mechanisms, which were shown by the functional and pathway enrichment analysis for the representative genes of each subtype. Besides, subtype-specific molecular patterns were also detected, such as subtype-specific clinical and mutation features. Finally, 12 functional genes and 13 functional edges could serve as prognosis biomarkers since they were associated with the survival rate of COAD.ConclusionsIn conclusion, the functional genes and interactions in the constructed functional network could be used as new biomarkers for COAD.