ISSN: 1449-2288International Journal of Biological Sciences
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Int J Biol Sci 2018; 14(8):833-842. doi:10.7150/ijbs.24816 This issue Cite
Research Paper
Genome-wide Analyses on Single Disease Samples for Potential Biomarkers and Biological Features of Molecular Subtypes: A Case Study in Gastric Cancer
1. Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
2. School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
3. Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.
4. Institute of Electronic and Information Engineering of UESTC in Guangdong, Dongguan, 523808, China.
5. Department of Biomedical Engineering, School of Automation and Information Engineering, Sichuan University of Science and Engineering, Zigong, 643000, China
Abstract
Purpose: Based on the previous 3 well-defined subtypes of gastric adenocarcinoma (invasive, proliferative and metabolic), we aimed to find potential biomarkers and biological features of each subtype.
Methods: The genome-wide co-expression network of each subtype of gastric cancer was firstly constructed. Then, the functional modules in each genome-wide co-expression network were divided. Next, the key genes were screened from each functional module. Finally, the enrichment analysis was performed on the key genes to mine the biological features of each subtype. Comparative analysis between each pair of subtypes was performed to find the common and unique features among different subtypes.
Results: A total of 207 key genes were identified in invasive, 215 key genes in proliferative, and 204 key genes in metabolic subtypes. Most key genes in each subtype were unique and new findings compared with that of the existing related researches. The GO and KEGG enrichment analyses for the key genes of each subtype revealed important biological features of each subtype.
Conclusions: For a subtype, most identified key genes and important biological features were unique, which means that the key genes can be used as the potential biomarker of a subtype, and each subtype of gastric cancer might have different occurrence and development mechanisms. Thus, different diagnosis and therapy methods should be applied to the invasive, proliferative and metabolic subtypes of gastric cancer.
Keywords: Genome-wide co-expression network, Molecular subtype, Key genes, Potential biomarker, Single disease samples
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