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Nucleic Acids Res. 2017 Jan 4;45(D1):D1060-D1063. doi: 10.1093/nar/gkw1029. Epub 2016 Nov 28.

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

Author information

1
Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China.
2
School of Finance and Statistics, East China Normal University, Shanghai 200241, China.
3
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.
4
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.

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.

PMID:
27899679
PMCID:
PMC5210528
DOI:
10.1093/nar/gkw1029
[Indexed for MEDLINE]
Free PMC Article

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