Campus Units
Electrical and Computer Engineering, Plant Pathology and Microbiology, Virtual Reality Applications Center, Bioinformatics and Computational Biology
Document Type
Article
Publication Version
Published Version
Publication Date
2012
Journal or Book Title
Nucleic Acids Research
Volume
40
Issue
D1
First Page
D1194
Last Page
D1201
DOI
10.1093/nar/gkr938
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 andArabidopsis. 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.
Rights
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright Owner
The Authors
Copyright Date
2011
Language
en
File Format
application/pdf
Recommended Citation
Dash, Sudhansu; Van Hemert, John L.; Hong, Lu; Wise, Roger P.; and Dickerson, Julie A., "PLEXdb: gene expression resources for plants and plant pathogens" (2012). Electrical and Computer Engineering Publications. 80.
https://lib.dr.iastate.edu/ece_pubs/80
Included in
Agricultural Science Commons, Agriculture Commons, Bioinformatics Commons, Computational Biology Commons, Microbiology Commons, Plant Pathology Commons, Systems and Communications Commons
Comments
This article is from Nucleic Acids Research 40 (2012): D1194–D1201, doi:10.1093/nar/gkr938. Posted with permission.