Background: In bioinformatic and clinical analysis, bioinformaticians often need to identify the key cancer-related genes, find out the signaling pathway and analyze the survival parameters in the development of cancer. Recent study has shown that the differentially expressed genes played an important role in finding out the disease-related genes. The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information, which gives opportunities to use this database to apply genetic analysis.
Methods: In this study, a general workflow to find out the key cancer-related genes and signaling pathway based on NCBI and gene expression omnibus was conducted. In this workflow, we implement four basic steps. The first step is to get the data from NCBI. And then, we select a subset of differentially expressed genes (DEGs) which is used to apply GO and KEGG pathway analysis in order to find out some specific cancer-related genes. The final step is to focus on survival analysis with specific cancer-related genes in KM-Plotter.
Results: Gastric cancer is one of the most common tumors in the digestive tract. The workflow of exploring cancer-related genes was established based on the NCBI database, which takes gastric cancer as an example, new genes related to gastric cancer were found through the significance test, the analysis of GO and KEGG signal pathways and the survival analysis of patient samples.
Conclusions: Through public database of GEO, we conduct a comprehensive analysis of the cancer-related gene on cancer groups and control groups. And then we analyze the key genes involved in biological processes and signaling pathways. In order to comprehensively analyze a certain gene expression in tumor characteristics and significance, we use the survival analysis tools to verify the genetic effect on cancer patients’ overall survival time. It provides theoretical support and guidance to further related researches about the gene.
Recommended citation: Zhikuan Quan. A general workflow to analyze key cancer-related genes based on NCBI illustrated by the case of gastric cancer[J]. International Core Journal of Engineering. 2018, 4(10): 45-51