Graphical methods for class prediction using dimension reduction techniques on DNA microarray data

• Published in: Bioinformatics 2003-07, Vol.19 (10), p.1252-1258
• Main Authors: BURA, Efstathia, PFEIFFER, Ruth M
• Format: Article
• Language: English
• Subjects: Algorithms; Biological and medical sciences; BRCA1 Protein - classification; BRCA1 Protein - genetics; BRCA2 Protein - classification; BRCA2 Protein - genetics; Breast Neoplasms - classification; Breast Neoplasms - genetics; Cluster Analysis; Computer Simulation; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; General aspects; Humans; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Oligonucleotide Array Sequence Analysis - methods; Regression Analysis; Reproducibility of Results; Sensitivity and Specificity; Sequence Analysis - methods
• ISSN: 1367-4803; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/btg150

We introduce simple graphical classification and prediction tools for tumor status using gene-expression profiles. They are based on two dimension estimation techniques sliced average variance estimation (SAVE) and sliced inverse regression (SIR). Both SAVE and SIR are used to infer on the dimension of the classification problem and obtain linear combinations of genes that contain sufficient information to predict class membership, such as tumor type. Plots of the estimated directions as well as numerical thresholds estimated from the plots are used to predict tumor classes in cDNA microarrays and the performance of the class predictors is assessed by cross-validation. A microarray simulation study is carried out to compare the power and predictive accuracy of the two methods. The methods are applied to cDNA microarray data on BRCA1 and BRCA2 mutation carriers as well as sporadic tumors from Hedenfalk et al. (2001). All samples are correctly classified.