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.

Comments

This article is from Nucleic Acids Research 40 (2012): D1194–D1201, doi:10.1093/nar/gkr938. Posted with permission.

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

Language

en

File Format

application/pdf

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