title: Processing of data generated by 2-dimensional gel electrophoresis for statistical analysis: missing data, normalization, and statistics.
abstract: Several high-throughput statistical methods were evaluated for processing data generated by two-dimensional polyacrylamide gel electrophoresis, including how to handle missing data, normalization, and statistical analysis of data obtained from 2-D gels. Quantile normalization combined with a nonparametric permutation test based on minimizing false discover rates gave the highest yield of proteins that changed with genotype and detected the anticipated 50% decrease in Mn-superoxide dismutase (MnSOD) protein levels in mitochondrial extracts obtained from MnSOD-deficient mice.
authors.affiliation: Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78284-7762, USA.
authors.forename: Jinsook
authors.initials: J
authors.lastname: Chang
authors.forename: Holly
authors.initials: H
authors.lastname: Van Remmen
authors.forename: Walter F
authors.initials: WF
authors.lastname: Ward
authors.forename: Fred E
authors.initials: FE
authors.lastname: Regnier
authors.forename: Arlan
authors.initials: A
authors.lastname: Richardson
authors.forename: John
authors.initials: J
authors.lastname: Cornell
mesh_terms: D000818:Animals; D001330:Electronic Data Processing / Q000379:methods*; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods* / Q000706:statistics & numerical data; D005838:Genotype; D051379:Mice; D008928:Mitochondria / Q000737:chemistry; D011506:Proteins / Q000032:analysis / Q000235:genetics; D040901:Proteomics / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013223:Statistics as Topic / Q000379:methods; D013482:Superoxide Dismutase / Q000032:analysis / Q000172:deficiency
chemical_list: D011506:Proteins; D013482:Superoxide Dismutase