CTexploreR, a package to explore CT genes
Axelle Loriot,Julie Devis,Anna Diacofotaki,Charles De Smet,Laurent Gatto
Cancer-Testis genes (CT genes), also referred as cancer-germline genes (CG genes), are a group a genes bearing a highly restricted expression pattern. They are normally expressed exclusively in male germ cells, but they become aberrantly activated in a wide variety of tumors. As germ cells do not express antigen presenting molecules, CT genes produce tumor-specific antigens and are extensively studied in the field of tumor immunotherapy. This group of genes comprise about 200 members that share common characteristics. Many of them belong to gene families (such as the archetypal MAGE gene family), they are enriched on X chromosome and they are often regulated by DNA methylation. Here we present CTexploreR, a package that re-defines the list of CT genes based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises their main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.