CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines

Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. While high-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multi-layer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to accommodate other types of omics data and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research. Author summary Recombinant proteins have dominated recent blockbuster therapeutic drugs, accounting for 11 of the top 15 drugs by sales. Chinese hamster ovary (CHO) cells are the most widely used expression system for biomanufacturing of many of these biotherapies. Thus, there is increasing interest in leveraging omics technologies for CHO cell line development, bioprocess optimization, and biotherapeutic product quality assessment. However, CHO cells have been largely ignored in the development of publicly available tools to facilitate comprehensive omics data analysis and management, despite being a ubiquitous research tool and biotherapeutic production host. To address the gap, we have recently developed a web-based tool, named "CHOmics", for the integrative and interactive data analysis and visualization specifically designed for CHO. This novel tool provides all-in-one solutions from raw data processing to pathway and gene analysis and offers considerable flexibility to customize analysis and visualization. It further allows for other omics data inputs and thereby enables multi-omics comparison. The open-source tool is freely available at http://www.chomics.org.