title: Correlation analysis of proteins responsive to Zn, Mn, or Fe deficiency in Arabidopsis roots based on iTRAQ analysis.
abstract: For discovering the functional correlation between the identified and quantified proteins by iTRAQ analysis, here we propose a correlation analysis method with cosine correlation coefficients as a powerful tool. iTRAQ analysis is a quantitative proteomics approach that enables identification and quantification of a large number of proteins. In order to obtain proteins responsive to Zn, Mn, or Fe mineral deficiency, we conducted iTRAQ analysis using a microsomal fraction of protein extractions from Arabidopsis root tissues. We identified and quantified 730 common proteins in three biological replicates with less than 1 % false discovery rate. To determine the role of these proteins in tolerating mineral deficiencies and their relation to each other, we calculated cosine correlation coefficients and represented the outcomes on a correlation map for visual understanding of functional relations among the identified proteins. Functionally similar proteins were gathered into the same clusters. Interestingly, a cluster of proteins (FRO2, IRT1, AHA2, PDR9/ABCG37, and GLP5) highly responsive to Fe deficiency was identified, which included both known and unknown novel proteins involved in tolerating Fe deficiency. We propose that the correlation analysis with the cosine correlation coefficients is a powerful method for finding important proteins of interest to several biological processes through comprehensive data sets.
authors.affiliation: Plant Global Education Project Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, 8916-5, Ikoma, 630-0192, Japan.
authors.forename: Sajad Majeed
authors.initials: SM
authors.lastname: Zargar
authors.forename: Masayuki
authors.initials: M
authors.lastname: Fujiwara
authors.forename: Shoko
authors.initials: S
authors.lastname: Inaba
authors.forename: Mami
authors.initials: M
authors.lastname: Kobayashi
authors.forename: Rie
authors.initials: R
authors.lastname: Kurata
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Ogata
authors.forename: Yoichiro
authors.initials: Y
authors.lastname: Fukao
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D000090463:Iron Deficiencies; D008345:Manganese / Q000172:deficiency; D013058:Mass Spectrometry / Q000379:methods; D018977:Micronutrients / Q000172:deficiency*; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism*; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction / Q000235:genetics; D015032:Zinc / Q000172:deficiency
chemical_list: D029681:Arabidopsis Proteins; D018977:Micronutrients; D020543:Proteome; D008345:Manganese; D015032:Zinc