title: PLEXdb: gene expression resources for plants and plant pathogens.
abstract: PLEXdb (http://www.plexdb.org), in partnership with community databases, supports comparisons of gene expression across multiple plant and pathogen species, promoting individuals and/or consortia to upload genome-scale data sets to contrast them to previously archived data. These analyses facilitate the interpretation of structure, function and regulation of genes in economically important plants. A list of Gene Atlas experiments highlights data sets that give responses across different developmental stages, conditions and tissues. Tools at PLEXdb allow users to perform complex analyses quickly and easily. The Model Genome Interrogator (MGI) tool supports mapping gene lists onto corresponding genes from model plant organisms, including rice and Arabidopsis. MGI predicts homologies, displays gene structures and supporting information for annotated genes and full-length cDNAs. The gene list-processing wizard guides users through PLEXdb functions for creating, analyzing, annotating and managing gene lists. Users can upload their own lists or create them from the output of PLEXdb tools, and then apply diverse higher level analyses, such as ANOVA and clustering. PLEXdb also provides methods for users to track how gene expression changes across many different experiments using the Gene OscilloScope. This tool can identify interesting expression patterns, such as up-regulation under diverse conditions or checking any gene's suitability as a steady-state control.
authors.affiliation: Virtual Reality Application Center, Crop Genome Informatics Lab, Electrical and Computer Engineering, Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA.
authors.forename: Sudhansu
authors.initials: S
authors.lastname: Dash
authors.forename: John
authors.initials: J
authors.lastname: Van Hemert
authors.forename: Lu
authors.initials: L
authors.lastname: Hong
authors.forename: Roger P
authors.initials: RP
authors.lastname: Wise
authors.forename: Julie A
authors.initials: JA
authors.lastname: Dickerson
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D017343:Genes, Plant; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D012984:Software; D059467:Transcriptome
references.citation: Bioinformatics. 2005 Feb 1;21(3):399-401
references.pmid: 15347571
references.citation: Plant J. 2011 May;66(4):553-63
references.pmid: 21299659
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D614-8
references.pmid: 15608273
references.citation: Bioinformatics. 2003 Mar 22;19(5):651-2
references.pmid: 12651724
references.citation: Database (Oxford). 2011 May 29;2011:bar022
references.pmid: 21624896
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D1009-14
references.pmid: 17986450
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D959-65
references.pmid: 18063570
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D456-8
references.pmid: 16381910
references.citation: Mol Plant Microbe Interact. 2009 Mar;22(3):311-20
references.pmid: 19245325
references.citation: Adv Bioinformatics. 2008;2008:420747
references.pmid: 19956698
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1149-55
references.pmid: 20935049
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1085-94
references.pmid: 21076153
references.citation: Plant Cell. 2004 Sep;16(9):2514-28
references.pmid: 15319481
references.citation: Mol Plant Microbe Interact. 2011 Sep;24(9):995-1000
references.pmid: 21585270
references.citation: BMC Bioinformatics. 2004 Aug 14;5:111
references.pmid: 15310390
references.citation: Comp Funct Genomics. 2002;3(2):137-42
references.pmid: 18628842
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1005-10
references.pmid: 21097893
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D885-90
references.pmid: 18940857
references.citation: Plant Methods. 2006 Jan 09;2:1
references.pmid: 16401339
references.citation: Methods Mol Biol. 2007;406:347-63
references.pmid: 18287702
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1002-4
references.pmid: 21071405