CEPICS: A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping

• Main Authors: Ran Duan, Lin Gao, Han Xu, Kuo Song, Yuxuan Hu, Hongda Wang, Yongqiang Dong, Chenxing Zhang, Songwei Jia
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2019-10-01
• Series: Frontiers in Genetics
• Subjects: data integration; multi-omics; cluster analysis; cancer subtypes; R package
• Online Access: https://www.frontiersin.org/article/10.3389/fgene.2019.00966/full

Cancer subtypes can improve our understanding of cancer, and suggest more precise treatment for patients. Multi-omics molecular data can characterize cancers at different levels. Up to now, many computational methods that integrate multi-omics data for cancer subtyping have been proposed. However, there are no consistent criteria to evaluate the integration methods due to the lack of gold standards (e.g., the number of subtypes in a specific cancer). Since comprehensive evaluation and comparison between different methods serves as a useful tool or guideline for users to select an optimal method for their own purpose, we develop a scalable platform, CEPICS, for comprehensively evaluating and comparing multi-omics data integration methods in cancer subtyping. Given a user-specified maximum number of subtypes, k-max, CEPICS provides (1) cancer subtyping results using up to five built-in state-of-the-art integration methods under the number of subtypes from two to k-max, (2) a report including the evaluation of each user-selected method and comparisons across them using clustering performance metrics and clinical survival analysis, and (3) an overall analysis of subtyping results by different methods representing a robust cancer subtype prediction for samples. Furthermore, users can upload subtyping results of their own methods to compare with the built-in methods. CEPICS is implemented as an R package and is freely available at https://github.com/GaoLabXDU/CEPICS.