An improved clear cell renal cell carcinoma stage prediction model based on gene sets

• Main Authors: Fangjun Li, Mu Yang, Yunhe Li, Mingqiang Zhang, Wenjuan Wang, Dongfeng Yuan, Dongqi Tang
• Format: Article
• Language: English
• Published: BMC 2020-06-01
• Series: BMC Bioinformatics
• Subjects: Feature selection; Machine learning; Clear cell renal cell carcinoma; Cancer stage
• Online Access: http://link.springer.com/article/10.1186/s12859-020-03543-0

Abstract Background Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma and accounts for cancer-related deaths. Survival rates are very low when the tumor is discovered in the late-stage. Thus, developing an efficient strategy to stratify patients by the stage of the cancer and inner mechanisms that drive the development and progression of cancers is critical in early prevention and treatment. Results In this study, we developed new strategies to extract important gene features and trained machine learning-based classifiers to predict stages of ccRCC samples. The novelty of our approach is that (i) We improved the feature preprocessing procedure by binning and coding, and increased the stability of data and robustness of the classification model. (ii) We proposed a joint gene selection algorithm by combining the Fast-Correlation-Based Filter (FCBF) search with the information value, the linear correlation coefficient, and variance inflation factor, and removed irrelevant/redundant features. Then the logistic regression-based feature selection method was used to determine influencing factors. (iii) Classification models were developed using machine learning algorithms. This method is evaluated on RNA expression value of clear cell renal cell carcinoma derived from The Cancer Genome Atlas (TCGA). The results showed that the result on the testing set (accuracy of 81.15% and AUC 0.86) outperformed state-of-the-art models (accuracy of 72.64% and AUC 0.81) and a gene set FJL-set was developed, which contained 23 genes, far less than 64. Furthermore, a gene function analysis was used to explore molecular mechanisms that might affect cancer development. Conclusions The results suggested that our model can extract more prognostic information, and is worthy of further investigation and validation in order to understand the progression mechanism.