PhenoPlasm: a database of disruption phenotypes for malaria parasite genes

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Author Spotlight: Identifying Compensatory Pathways in Malaria Parasites Containing Hypomorphic Allele of Essential Protein Kinases
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Author Spotlight: Identifying Compensatory Pathways in Malaria Parasites Containing Hypomorphic Allele of Essential Protein Kinases

Published on: November 22, 2024

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Theo Sanderson1, Julian C Rayner1

  • 1Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

Wellcome Open Research
|July 28, 2017
PubMed

Insights

PhenoPlasm is a new database that consolidates malaria parasite transfection data. It enables cross-species analysis of gene functions, identifying essential proteins like RAP-domain containing proteins for parasite survival.

Area of Science:

  • Malaria research
  • Parasitology
  • Genetics

Background:

  • Over 3,151 genes have been targeted in malaria parasites across five species.
  • Rodent malaria transfection data is systematized, but human malaria parasite data is fragmented.
  • A need exists for a centralized resource for analyzing Plasmodium transfection phenotypes.

Purpose of the Study:

  • To build PhenoPlasm, a comprehensive database of Plasmodium transfection phenotypes.
  • To facilitate systematic, cross-species analysis of experimental genetic data.
  • To link gene IDs with citation-backed phenotypes for Plasmodium parasites.

Main Methods:

  • Developed PhenoPlasm (http://www.phenoplasm.org) to curate and integrate transfection phenotype data.
  • Populated the database with 367 P. falciparum genes from 176 publications.
  • Incorporated existing rodent Plasmodium data from RMgmDB and PlasmoGEM.
  • Implemented ortholog mapping for cross-species gene comparison.

Main Results:

  • PhenoPlasm centralizes all available P. falciparum transfection data.
  • The database includes data for P. falciparum and rodent Plasmodium species.
  • Ortholog mapping allows researchers to explore gene function across different Plasmodium species.
  • Database utility demonstrated by identifying RAP-domain proteins as crucial for parasite survival.

Conclusions:

  • PhenoPlasm is the first comprehensive database for Plasmodium transfection phenotypes.
  • The database enables systematic analysis and discovery across Plasmodium species.
  • PhenoPlasm supports collaborative data sharing and expansion.
  • Identified RNA-binding domain abundant in Apicomplexa (RAP)-domain proteins as vital for parasite survival.
Keywords:
MalariaPlasmodiumdatabasegeneticknock-outphenotype

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