EuPathDB: the eukaryotic pathogen genomics database resource

Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

EuPathDB resources have been expanded to include FungiDB (http://fungidb.org) (8) , which supports fungi and oomycetes, and HostDB (http://hostdb.org), for interrogation of host responses to infection. HostDB supports host data obtained during infections by organisms supported by EuPathDB's 10 parasite lineage-specific databases. Minot et al. (9) , for example, infected murine macrophages with 29 Toxoplasma gondii strains and collected mixed parasitehost samples for RNA sequencing. Reads that align to the T. gondii genome are integrated into ToxoDB whereas HostDB houses those sequencing reads that align to the M. musculus genome. Because all EuPathDB databases employ the same data analysis pipelines, search strategy system, visualization and analysis tools, the T. gondii and M. musculus data can be compared. For example, one can easily identify parasite genes that are differentially expressed between two T. gondii strains from ToxoDB as well as host genes that are differentially expressed during infection with the same two strains from HostDB. Enrichment analyses and comparison of these lists offers insights into host-pathogen interactions and responses.