Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice

Frontiers in Plant Science
Joao B de Abreu Neto, Michael Frei

Abstract

Plants are exposed to a wide range of abiotic stresses (AS), which often occur in combination. Because physiological investigations typically focus on one stress, our understanding of unspecific stress responses remains limited. The plant redox homeostasis, i.e., the production and removal of reactive oxygen species (ROS), may be involved in many environmental stress conditions. Therefore, this study intended to identify genes, which are activated in diverse AS, focusing on ROS-related pathways. We conducted a meta-analysis (MA) of microarray experiments, focusing on rice. Transcriptome data were mined from public databases and fellow researchers, which represented 36 different experiments and investigated diverse AS, including ozone stress, drought, heat, cold, salinity, and mineral deficiencies/toxicities. To overcome the inherent artifacts of different MA methods, data were processed using Fisher, rOP, REM, and product of rank (GeneSelector), and genes identified by most approaches were considered as shared differentially expressed genes (DEGs). Two MA strategies were adopted: first, datasets were separated into shoot, root, and seedling experiments, and these tissues were analyzed separately to identify shared DEGs. Second,...Continue Reading

References

Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Apr 25, 2003·Methods in Molecular Biology·Gordon K SmythTerry Speed
Jun 27, 2003·Functional & Integrative Genomics·Samuel P HazenJoel A Kreps
Jul 12, 2003·Bioinformatics·Jung Kyoon ChoiOok Joon Yoo
Aug 3, 2005·PLoS Medicine·John P A Ioannidis
Mar 15, 2006·BMC Bioinformatics·Richard J Fox, Matthew W Dimmic
Oct 20, 2006·Statistical Applications in Genetics and Molecular Biology·Robert P DeCondeRuth Etzioni
May 24, 2008·Antioxidants & Redox Signaling·Simon FourquetMichel B Toledano
Jul 17, 2008·Comparative and Functional Genomics·Pankaj JaiswalSusan McCouch
Jul 17, 2008·Comparative and Functional Genomics·Daniel von Wachter
Sep 5, 2008·PLoS Medicine·Adaikalavan RamasamyDouglas G Altman
Jun 25, 2009·The Plant Journal : for Cell and Molecular Biology·Pinja JaspersJaakko Kangasjärvi
Aug 15, 2009·Briefings in Bioinformatics·Anne-Laure Boulesteix, Martin Slawski
Aug 29, 2009·Plant, Cell & Environment·Gad MillerRon Mittler
May 4, 2010·Nucleic Acids Research·Zhou DuZhen Su
Sep 28, 2010·Plant Physiology and Biochemistry : PPB·Sarvajeet Singh Gill, Narendra Tuteja
Nov 4, 2010·Plant Physiology·Christine H Foyer, Shigeru Shigeoka
Apr 13, 2011·Trends in Plant Science·Ron MittlerFrank Van Breusegem
Dec 14, 2011·Proceedings of the National Academy of Sciences of the United States of America·Shimpei UraguchiToru Fujiwara
Jan 21, 2012·Nucleic Acids Research·George C TsengEleanor Feingold
Feb 16, 2012·The Journal of Biological Chemistry·Takanori MarutaShigeru Shigeoka
Mar 16, 2012·Plant Physiology and Biochemistry : PPB·Chiara PucciarielloPierdomenico Perata
Sep 12, 2012·BMC Plant Biology·Tian-Li MaYi Wang
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva

❮ Previous
Next ❯

Methods Mentioned

BETA
environmental stresses

Software Mentioned

REM
LIMMA
ArrayQualityMetrics
MA
Affy
AggMC
GeneSelector
metaDE
STRING
R

Related Concepts

Related Feeds

Anemia

Anemia develops when your blood lacks enough healthy red blood cells. Anemia of inflammation (AI, also called anemia of chronic disease) is a common, typically normocytic, normochromic anemia that is caused by an underlying inflammatory disease. Here is the latest research on anemia.