PHI-base: the pathogen–host interactions database

Abstract

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. PHI-base also curates literature describing specific gene alterations that did not affect the disease interaction phenotype, in order to provide complete datasets for comparative purposes. Viruses are not included, due to their extensive coverage in other databases. In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases. The release of PHI-base version 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 genes from 268 pathogens, tested on 210 hosts in 13,801 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species consist of approximately 60% plants (split 50:50 between cereal and non-cereal plants), and 40% other species of medical and/or environmental importance. The information available on pathogen effectors has risen by more than a third, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release. We also briefly describe the future direction of the PHI-base project, and some existing problems with the PHI-base curation process.

Dual species dynamic transcripts reveal the interaction mechanisms between Chrysanthemum morifolium and Alternaria alternata

“…A series of highly correlated modules between C. morifolium and A. alternata were identi ed. PRGdb is a bioinformatics platform for plant resistance gene analysis [24], and PHI-base contains molecular and biological information on genes that have been proven to affect the outcome of pathogenhost interactions [25]. The regulatory network of key genes annotated in PRGdb or PHI-base at the three infection stages were visualized using the Cytoscape software.…”

“…The degree of GO term enrichment was similar for the three inoculation time points, and DEGs were divided into 54 functional categories according to biological processes (25), cellular components (16), and molecular functions (13). The most signi cantly enriched biological processes were "regulation of transcription, DNA-templated", "carbohydrate metabolic process", and "translation"; the most significantly enriched cellular components were "cytoplasm", "ribosome", and "chloroplast", while "protein serine/threonine kinase activity", "nucleic acid binding" and "oxidoreductase activity" occupied the important positions in molecular functions ( Figure 2D).…”

“…The Plant Resistance Genes database (PRGdb; http://prgdb.org) is a bioinformatics platform for plant resistance gene analysis [24]. The pathogen-host interactions database (PHI-base: www.phi-base.org) contains molecular and biological information on genes which have been proven to affect the outcome of host-pathogen interactions [25]. Key genes from the highly correlated modules were examined for further analyses.…”

Accurate plant pathogen effector protein classification ab initio with deepredeff, an ensemble of convolutional neural networks

“…Sequence data were collected from the PHI-Base database version 4.8 (Urban et al, 2019) by accessing a text dump of the data prepared on request by the PHI-Base team, the file can be accessed at https://github.com/PHI-base/data/blob/master/releases/phi-base_current.csv. The pipeline in Figure 1 outlines the steps used.…”

“…The performance of the trained classifiers is dependent on the quality of the input training data, so it was important that we collected as high a quality set of annotated effectors as possible. To this end we used PHI-Base (Urban et al, 2019) as our primary sequence origin. Sequences in PHI-Base are human curated from the literature and have therefore been noted in experimental studies.…”