CGSEA: A Flexible Tool for Evaluating the Associations of Chemicals with Complex Diseases

The etiology of many human complex diseases or traits involves interactions between chemicals and genes that regulate important physiological processes. It has been well documented that chemicals can contribute to disease development through affecting gene expression in vivo. In this study, we developed a flexible tool CGSEA for scanning the candidate chemicals associated with complex diseases or traits. CGSEA only need genome-wide summary level data, such as transcriptome-wide association studies (TWAS) and mRNA expression profiles. CGSEA was applied to the GWAS summaries of attention deficiency/hyperactive disorder, (ADHD), autism spectrum disorder (ASD) and cervical cancer. CGSEA identified several significant chemicals, which have been demonstrated to be involved in the development or treatment of ADHD, ASD and cervical cancer. The CGSEA program and user manual are available at https://github.com/ChengSQXJTU/CGSEA.