title: AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis.
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.
authors.affiliation: Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.|School of Finance and Statistics, East China Normal University, Shanghai 200241, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Lv
authors.affiliation: Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.
authors.forename: Yiheng
authors.initials: Y
authors.lastname: Lan
authors.affiliation: Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.
authors.forename: Huan
authors.initials: H
authors.lastname: Wang
authors.affiliation: Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.
authors.forename: Xia
authors.initials: X
authors.lastname: Pan
authors.affiliation: Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China PLI6@mgh.harvard.edu.
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.affiliation: Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China tlshi@bio.ecnu.edu.cn.
authors.forename: Tieliu
authors.initials: T
authors.lastname: Shi
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies / Q000379:methods; D018745:Genome, Plant; D005838:Genotype; D058977:Molecular Sequence Annotation; D010641:Phenotype; D015398:Signal Transduction; D064878:Web Browser