title: PlantPReS: A database for plant proteome response to stress.
abstract: About 75% of plant yield potential has been estimated to be lost to environmental stresses, even in developed agricultures. To facilitate the biotechnological improvement of crop productivity, genes and proteins that control crop adaptation to a wide range of environments will need to be identified. Due to the challenges faced in text/data mining, there is a large gap between the data available to researchers and the hundreds of published plant stress proteomics articles. Plant stress proteome database (PlantPReS; www.proteome.ir) is an open online proteomic database, which currently (as of October 2015) comprises >20,413 entries from 456 manually curated articles, and contains >10,600 unique stress responsive proteins. Since every aspect of the experiments, including protein name, accession number, plant type, tissue, stress types, organelles, and developmental stage has been digitized, experimental data can be rapidly accessed and integrated. Furthermore, PlantPReS enables researchers to perform multiple analyses on the database using the filtration mode, and the results of each query indicate a series of proteins for which a set of selected criteria is met. The query results can be displayed in either text or graphical format.
  
  
  
  The promise of text and data mining to facilitate and enhance research fundamentally has not yet been achieved, mainly because great numbers of stress-associated proteins are not deposited in databases. PlantPReS is a valuable database for the vast majority of researchers working in proteomics and plant stress areas. It has a user-friendly interface with a number of useful features, including a search engine, analysis tools, gene ontology, a function for cross-referencing useful external databases, and the expression pattern of stress associated proteins.
authors.affiliation: Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran; Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
authors.forename: Seyed Ahmad
authors.initials: SA
authors.lastname: Mousavi
authors.affiliation: Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran.
authors.forename: Farhad Movahedi
authors.initials: FM
authors.lastname: Pouya
authors.affiliation: Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran.
authors.forename: Mohammad Reza
authors.initials: MR
authors.lastname: Ghaffari
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mirzaei
authors.affiliation: Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran.
authors.forename: Akram
authors.initials: A
authors.lastname: Ghaffari
authors.affiliation: Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Alikhani
authors.affiliation: Computer Science Department, University of California, Davis, Davis, CA, United States.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Ghareyazie
authors.affiliation: National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan.
authors.forename: Setsuko
authors.initials: S
authors.lastname: Komatsu
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Haynes
authors.affiliation: Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran; Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran. Electronic address: h_salekdeh@abrii.ac.ir.
authors.forename: Ghasem Hosseini
authors.initials: GH
authors.lastname: Salekdeh
mesh_terms: D000222:Adaptation, Physiological; D018556:Crops, Agricultural; D030562:Databases, Protein; D018506:Gene Expression Regulation, Plant; D020407:Internet; D010940:Plant Proteins / Q000235:genetics / Q000502:physiology*; D020543:Proteome; D040901:Proteomics; D057386:Search Engine; D013312:Stress, Physiological / Q000235:genetics; D014584:User-Computer Interface
chemical_list: D010940:Plant Proteins; D020543:Proteome
keywords: Database; Plant stress; Proteomics