A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Liquet, Benoit ^a,b,e   Cao, Kim Anh Lê ^c   Hocini, Hakim ^d,e   Thiébaut, Rodolphe ^a,b,e  

^a UNIVERSITÉ DE BORDEAUX   (France)

^b INSERM   (France)

^c UNIVERSITY OF QUEENSLAND   (Australia)

^d UNIVERSITÉ PARIS EST CRÉTEIL   (France)

^e ANRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL VARIATION; BIOMARKER SELECTIONS; CLASSIFICATION ERROR RATE; INTEGRATIVE ANALYSIS; MULTI-LEVEL ANALYSIS; MULTIVARIATE APPROACH; MULTIVARIATE METHODS; REPEATED MEASUREMENTS;

BIOMARKERS; GENE EXPRESSION; PHYSIOLOGY; VACCINES;

EXPERIMENTS;

HUMAN IMMUNODEFICIENCY VIRUS;

BIOLOGICAL MARKER; CYTOKINE; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; TRANSCRIPTOME;

ARTICLE; CLINICAL TRIAL (TOPIC); CLUSTER ANALYSIS; COMPUTER SIMULATION; DISCRIMINANT ANALYSIS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETICS; HUMAN; IMMUNOLOGY; METHODOLOGY; MULTIVARIATE ANALYSIS;

AIDS VACCINES; BIOLOGICAL MARKERS; CLINICAL TRIALS AS TOPIC; CLUSTER ANALYSIS; COMPUTER SIMULATION; CYTOKINES; DISCRIMINANT ANALYSIS; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; MULTIVARIATE ANALYSIS; TRANSCRIPTOME;

MLCS; MLOWN;

EID: 84870418540     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-325     Document Type: Article

References (31)

1. Storey JD, Xiao W, Leek JT, Tompkins RG, Davis RW. Significance analysis of time course microarray experiments. Proc National Acad Sci USA 2005, 102(36):12837-12842.
2. Li H, Wood C, Getchell T, Getchell M, Stromberg A. Analysis of oligonucleotide array experiments with repeated measures using mixed models. BMC Bioinformatics 2004, 5:209. [http://www.biomedcentral.com/1471-2105/5/209].
3. Karlovich C, Duchateau-Nguyen G, Johnson A, McLoughlin P, Navarro M, Fleurbaey C, Steiner L, Tessier M, Nguyen T, Wilhelm-Seiler M, Caulfield J. A longitudinal study of gene expression in healthy individuals. BMC Med Genomics 2009, 2:33.
4. Palermo RE, Patterson LJ, Aicher LD, Korth MJ, Robert-Guroff M, Katze MG. Genomic Analysis Reveals Pre- and Postchallenge Differences in a Rhesus Macaque AIDS Vaccine Trial: Insights into Mechanisms of Vaccine Efficacy. J Virol January 15 2011, 85(2):1099-1116.
5. Kitano H. Computational Systems Biology. Nature 6912, 420:206-210.
6. Chun H, Keleş S. Sparse partial least squares regression for simultaneous dimension reduction and variable selection. J R Stat Soc: Series B (Statistical Methodology) 2010, 72:3-25.
7. Lê Cao KA, Rossouw D, Robert-Granié C, Besse P. Sparse PLS Variable Selection when Integrating Omics data. Stat App Mol Biol 2008, 7(1):37.
8. Lê Cao KA, Martin P, Robert-Granié C, Besse P. Sparse canonical methods for biological data integration: application to a cross-platform study. BMC Bioinformatics 2009, 10(34).
9. Parkhomenko E, Tritchler D, Beyene J. Sparse canonical correlation analysis with application to genomic data integration. Stat App Genet Mol Biol 2009, 8(1):1-34.
10. Waaijenborg S, de Witt Hamer V, Philip C, Zwinderman A. Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis. Stat App Genet Mol Biol 2008, 7(3).
11. Witten DM, Tibshirani R, Hastie T. A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 2009, 10(3):515-534.
12. Tenenhaus A, Tenenhaus M. Regularized Generalized Canonical Correlation Analysis. Psychometrika 2011, 76(2):257-284.
13. Morine M, Tierney A, van Ommen B, Daniel H, Toomey S, Gjelstad I, Gormley I, Pérez-Martinez P, Drevon C, López-Miranda J, et al. Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health. PLoS comput biol 2011, 7(11):e1002223.
14. Rose M, Rose T, Pariasca-Tanaka J, Wissuwa M, et al. Revisiting the role of organic acids in the bicarbonate tolerance of zinc-efficient rice genotypes. Funct Plant Biol 2011, 38(6):493-504.
15. Barker M, Rayens W. Partial least squares for discrimination. J Chemom 2003, 17(3):166-173.
16. Lê Cao K, Boitard S, Besse P. Sparse PLS Discriminant Analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC bioinformatics 2011, 12:253.
17. Dauwe R, Holliday J, Aitken S, Mansfield S. Metabolic dynamics during autumn cold acclimation within and among populations of Sitka spruce (Picea sitchensis). New Phytologist 2012, 194(1):192-205.
18. de Noord OE, Theobald EH. Multilevel component analysis and multilevel PLS of chemical process data. J Chemom 2005, 19(5-7):301-307. [http://dx.doi.org/10.1002/cem.933].
19. Westerhuis JA, van Velzen EJ, Hoefsloot HC, Smilde AK. Multivariate paired data analysis: multilevel PLSDA versus OPLSDA. Metabolomics 2010, 6:119-128. [http://dx.doi.org/10.1007/s11306-009-0185-z].
20. van Velzen EJJ, Westerhuis JA, van Duynhoven JPM, van Dorsten FA, Hoefsloot HCJ, Jacobs DM, Smit S, Draijer R, Kroner CI, Smilde AK. Multilevel Data Analysis of a Crossover Designed Human Nutritional Intervention Study. J Proteome Res 2008, 7(10):4483-4491.
21. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate : A Practical and Powerful Approach to Multiple Testing. J R Stat Soc. Series B 2009, 57:289-300.
22. Ambroise C, McLachlan G. Selection bias in gene extraction on the basis of microarray gene-expression data. Proc National Acad Sci 2002, 99(10):6562.
23. Wold H. Multivariate Analysis. Academic Press 1966, Wiley, krishnaiah, p.r. (ed.) edition, New York.
24. Boulesteix A, Strimmer K. Partial least squares: a versatile tool for the analysis of high-dimensional genomic data. Briefings in Bioinf 2007, 8:32.
25. Vinzi V, Trinchera L, Amato S. PLS path modeling: from foundations to recent developments and open issues for model assessment and improvement. Handbook of Partial Least Squares 2010, chapter 2:47-82.
26. Salmon-Céron D, Durier C, Desaint C, Cuzin L, Surenaud M, Hamouda N, Lelièvre J, Bonnet B, Pialoux G, Poizot-Martin I, Aboulker J, Lévy Y, Launay O, trial group AV. Immunogenicity and safety of an HIV-1 lipopeptide vaccine in healthy adults: a phase 2 placebo-controlled ANRS trial. AIDS 2010, 24(14):2211-2223.
27. Dudoit S, Shafer JP, Boldrick JC. Multiple Hypothesis Testing in Microarray Experiments. Stat Sci 2003, 18:71-103.
28. Pinheiro J, Bates D. Mixed-Effects Models in S and S-PLUS. New York 2000, Springer, USA.
29. Kenward MG, Roger JH. Small Sample Inference for Fixed Effects from Restricted Maximum Likelihood. Biometrics 1997, 53(3):983-997.
30. Schaalje GB, McBride JB, Fellingham GW. Adequacy of Approximations to Distributions of Test Statistics in Complex Mixed Linear Models. J Agric, Biol, and Environ Stat 2002, 7(4):512-524.
31. Raymond AD, Gekonge B, Giri MS, Hancock A, Papasavvas E, Chehimi J, Kossevkov AV, Nicols C, Yousef M, Mounzer K, Shull J, Kostman J, Showe L, Montaner LJ. Increased metallothionein gene expression, zinc, and zinc-dependent resistance to apoptosis in circulating monocytes during HIV viremia. J Leukocyte Biol 2010, 88(3):589-596.