PHI-base: a new database for pathogen host interactions

Abstract

To utilize effectively the growing number of verified genes that mediate an organism's ability to cause disease and/or to trigger host responses, we have developed PHI-base. This is a web-accessible database that currently catalogs 405 experimentally verified pathogenicity, virulence and effector genes from 54 fungal and Oomycete pathogens, of which 176 are from animal pathogens, 227 from plant pathogens and 3 from pathogens with a fungal host. PHI-base is the first on-line resource devoted to the identification and presentation of information on fungal and Oomycete pathogenicity genes and their host interactions. As such, PHI-base is a valuable resource for the discovery of candidate targets in medically and agronomically important fungal and Oomycete pathogens for intervention with synthetic chemistries and natural products. Each entry in PHI-base is curated by domain experts and supported by strong experimental evidence (gene/transcript disruption experiments) as well as literature references in which the experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, we have annotated genes using controlled vocabularies (Gene Ontology terms, Enzyme Commission Numbers and so on), and provide links to other external data sources (e.g. NCBI taxonomy and EMBL). We welcome new data for inclusion in PHI-base, which is freely accessed at .

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

“…BLAST searching against the FUNCAT database and PHI (pathogen–host interaction) provided a global view of the gene functions (Ruepp et al 2004; Winnenburg et al 2006). Statistics for the gene abundance were performed by t -test and was corrected by false discovery rate (FDR) test with the p  < 0.01.…”

Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics

“…Genome analyses facilitate the isolation and characterization of genes and regulatory mechanisms that control mycotoxin production. The in planta upregulation of candidate effectors, genes involved in secondary metabolite biosynthesis, as well as the pathogen-host interaction database (PHI-base) 20 genes suggests a list of candidate virulence factors that may play important roles in pathogenicity. Overall, this genome project establishes foundation for the rice Ustilaginoidea pathosystem as a primary target for elucidating the interaction between hosts and biotrophic fungal pathogens.…”

The Prediction and Analysis of Inter- and Intra-Species Protein-Protein Interaction

“…It collects information for 98 pathogens of two hosts, human, and mouse (Xiang et al, 2007). PHI-Base contains information for 405 fungal, oomycete, and bacterial genes which participate in pathogenicity, virulence, and induction of disease resistance Winnenburg et al, 2006). 176 of these genes are from animal pathogens, 227 from plant pathogens, and 3 from pathogens of fungi.…”