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PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

Martin Urban1, Alayne Cuzick2, Kim Rutherford3

  • 1Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK Martin.Urban@rothamsted.ac.uk.

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Summary

The pathogen-host interactions database (PHI-base) Version 4.2 offers enhanced data and search functions for pathogen-host interaction genes. This updated resource aids researchers in understanding gene roles in disease outcomes across various organisms.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Pathogen-host interactions are crucial for disease development.
  • Understanding the genetic basis of these interactions is vital for disease control.
  • Existing databases often lack comprehensive, curated data on genes affecting pathogen-host interactions.

Purpose of the Study:

  • To describe the revised PHI-base Version 4 data platform.
  • To introduce improved search, filtering, and data display functionalities.
  • To provide a comprehensive resource for pathogen-host interaction gene data.

Main Methods:

  • Expert curation of molecular and biological information from peer-reviewed literature.
  • Inclusion of genes affecting disease phenotypes and those that do not, for comparative analysis.
  • Development of PHI-BLAST search and PHI-Canto for direct author curation.

Main Results:

  • PHI-base Version 4.2 contains data from 2219 references, covering 4460 genes, 264 pathogens, and 176 hosts.
  • Data includes 8046 interactions, with nearly equal representation of prokaryotic and eukaryotic pathogens.
  • Host species are predominantly plants (~70%), with others of medical/environmental importance (~30%).
  • New data types include direct targets of pathogen effector proteins.

Conclusions:

  • PHI-base Version 4.2 provides a significantly expanded and enhanced resource for studying pathogen-host interactions.
  • Improved functionalities facilitate data retrieval and analysis for researchers.
  • The database supports comparative genomics and understanding effector-host interactions.