Abstract
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 with 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.
Highlights
Protein functional annotation and the protein networks including protein–protein interactions and regulatory relations are essential for understanding the underlying mechanism of the biological system
An integrated database resource for protein interaction network and functional annotation proteome.(http://www.megabionet.org/atpid) The predicted Arabidopsis interactome resource(http://www.cls.zju.edu.cn/pair/) [24] A database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.(http://www.arabidopsis.org) [25] An interaction repository with data compiled through comprehensive curation efforts.(http://thebiogrid.org/) [26] A database of predicted functional associations between proteins.(http://string-db.org/) [27]
We have made great efforts to provide a significantly improved resource for genotype–phenotype associations, which could serve as a resource for experimental design and facilitate genome-wide systematical studies in Arabidopsis
Summary
Protein functional annotation and the protein networks including protein–protein interactions and regulatory relations are essential for understanding the underlying mechanism of the biological system. AtPID is a comprehensive data resource developed using Arabidopsis thaliana as the model system for protein interactions and functional annotation.
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