AtPID: a genome-scale resource for genotype–phenotype associations in Arabidopsis

Qi Lv, Yiheng Lan, Yan Shi, Huan Wang, Xia Pan, Peng Li, Tieliu Shi
2016 Nucleic Acids Research  
AtPID (Arabidopsis thaliana Protein Interactome Database, available at http://www.megabionet.org/ atpid) is an integrated database resource for protein interaction network and functional annotation. In the past few years, we collected 5564 mutants with significant morphological alterations and manually curated them to 167 plant ontology (PO) morphology categories. These single/multiple-gene mutants were indexed and linked to 3919 genes. After integrated these genotype-phenotype associations
more » ... the comprehensive protein interaction network in AtPID, we developed a Naïve Bayes method and predicted 4457 novel high confidence gene-PO pairs with 1369 genes as the complement. Along with the accumulated novel data for protein interaction and functional annotation, and the updated visualization toolkits, we present a genome-scale resource for genotype-phenotype associations for Arabidopsis in AtPID 5.0. In our updated website, all the new genotype-phenotype associations from mutants, protein network, and the protein annotation information can be vividly displayed in a comprehensive network view, which will greatly enhance plant protein function and genotype-phenotype association studies in a systematical way.
doi:10.1093/nar/gkw1029 pmid:27899679 pmcid:PMC5210528 fatcat:gm2fslshavgrrl37uptxgw5mtq