Additional file 1 of Functional conservation in genes and pathways linking ageing and immunity

Additional file 1: Table S1. Immuno-ageing, longevity/ageing, and immunity genes. To define immuno-ageing genes (‘ImmAg’ sheets) we assembled all currently known immunity and longevity/ageing genes (‘Imm’ and ‘Ag’ sheets) from various databases and identified genes occurring in both traits (see ‘Summary’ tab). This was done for two invertebrates, C. elegans and D. melanogaster (‘Cele’ and ‘Dmel’ sheets), and two mammals, M. musculus and H. sapiens (‘Mouse’ and ‘Human’ sheets). Ageing genes were obtained from the GO term ‘aging’ (GO:0007568), the KEGG pathway annotation ‘Longevity regulating pathway’ (KEGG id: 04213), and two ageing databases GenAge and AgeFactDB. Immunity genes were compiled from the GO term ‘immune system process‘ (GO:0002376), multiple immune-related KEGG pathways (for D. melanogaster only available KEGG id: 04624; while for mammals we used: 04640, 04610, 04611, 04620, 04621, 04622, 04623, 04625, 04650, 04612, 04660, 04658, 04659, 04657, 04662, 04664, 04666, 04670, 04672, and 04062), and the three immunity databases insect innate immunity database IIIDB, InnateDB, and immunome knowledge base (IKB). Genes from GO and KEGG were obtained using the biomaRt package in R, while genes from databases were downloaded from the corresponding websites. We added additional annotations (such as IDs from multiple databases) using biomaRt, and the species-specific browsers WormBase for C. elegans, FlyBase for D. melanogaster, MGI for M. musculus, and HGNC for H. sapiens. For AgeFactDB, we excluded all genes for which the experimental evidence was annotated as ‘putative’ or ‘no’. Annotations were obtained in January 2019 for IIIDB and Immunome, and August 2020 for all others. Additional genes with clear effects on immunity and ageing, which we found reviewing the literature, were manually added for C. elegans and D. melanogaster (‘handcurated’ column; references below). The number of genes obtained from each database are given in the ‘Summary’ sheet. The column ‘Longevity’ in the gene lists indicates whether a gene is beneficial (pro) or detrimental (anti) for lifespan or had no effect (none) as defined by the GenAge database.