Detecting intergene correlation changes in microarray analysis: A new approach to gene selection

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Hu, Rui ^a   Qiu, Xing ^a   Glazko, Galina ^a   Klebanov, Lev ^b   Yakovlev, Andrei ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

^b CHARLES UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL CONDITIONS; DIFFERENTIAL EXPRESSIONS; MICROARRAY ANALYSIS; MICROARRAY TECHNOLOGIES; MULTIDIMENSIONAL INFORMATION; RESAMPLING TECHNIQUE; SELECTION CRITERIA; SELECTION PROCEDURES;

GENE EXPRESSION;

ALGORITHM; ARTICLE; BIOLOGY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; METHODOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 62749083987     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-20     Document Type: Article

References (26)

1. Dudoit S Shaffer J Boldrick J Multiple hypothesis testing in microarray experiments Statistical Science 2003, 18:71-103.
2. Simon RM Korn EL McShane LM Radmacher MD Wright GW Zhao Y Design and Analysis of DNA Microarray Investigations Springer Verlag 2003.
3. Klebanov L Jordan C Yakovlev A A new type of stochastic dependence revealed in gene expression data Stat Appl Genet Mol Biol 2006, 5. Article7 16646871
4. Tian L Greenberg SA Kong SW Altschuler J Kohane IS Park PJ Discovering statistically significant pathways in expression profiling studies Proc Natl Acad Sci USA 2005, 102(38):13544-13549. 1200092 16174746
5. Yeoh EJ Ross ME Shurtleff SA Williams WK Patel D Mahfouz R Behm FG Raimondi SC Relling MV Patel A Cheng C Campana D Wilkins D Zhou X Li J Liu H Pui CH Evans WE Naeve C Wong L Downing JR Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling Cancer Cell 2002, 1(2):133-143. 12086872
6. Dai M Wang P Boyd AD Kostov G Athey B Jones EG Bunney WE Myers RM Speed TP Akil H Watson SJ Meng F Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data Nucleic Acids Res 2005, 33(20):e175. 1283542 16284200
7. Szabo A Boucher K Carroll W Klebanov L Tsodikov A Yakovlev A Variable selection and pattern recognition with gene expression data generated by the microarray technology Mathematical Biosciences 2002, 176:71-98. 11867085
8. Szabo A Boucher K Jones D Tsodikov AD Klebanov LB Yakovlev AY Multivariate exploratory tools for microarray data analysis Biostatistics 2003, 4(4):555-567. 14557111
9. Xiao Y Frisina R Gordon A Klebanov L Yakovlev A Multivariate search for differentially expressed gene combinations BMC Bioinformatics 2004, 5:164. 529250 15507138
10. Klebanov L Gordon A Xiao Y Land H Yakovlev A A permutation test motivated by microarray data analysis Computational Statistics and Data Analysis 2005.
11. Gordon A Glazko G Qiu X Yakovlev A Control of the Mean Number of False Discoveries, Bonferroni, and Stability of Multiple Testing The Annals of Applied Statistics 2007, 1:179-190.
12. Jaeger J Sengupta R Ruzzo WL Improved gene selection for classification of microarrays Pac Symp Biocomput 2003, 53-64. 12603017
13. Goeman JJ Geer van de SA de Kort F van Houwelingen HC A global test for groups of genes: Testing association with a clinical outcome Bioinformatics 2004, 20:93-99. 14693814
14. Geman D d'Avignon C Naiman DQ Winslow RL Classifying gene expression profiles from pairwise mRNA comparisons Stat Appl Genet Mol Biol 2004, 3. Article19 1989150 16646797
15. Lai Y Wu B Chen L Zhao H A statistical method for identifying differential gene-gene co-expression patterns Bioinformatics 2004, 20(17):3146-3155. 15231528
16. Shedden K Taylor J Differential correlation detects complex associations between gene expression and clinical outcomes in lung adenocarcinomas Methods of Microarray Data Analysis IV 2005, 121-131.
17. Laan van der MJ Birkner MD Hubbard AE Empirical Bayes and resampling based multiple testing procedure controlling tail probability of the proportion of false positives Stat Appl Genet Mol Biol 2005, 4. Article29 16646847
18. Lu Y Liu P Xiao P Deng H Hotelling's T 2 multivariate profiling for detecting differential expression in microarrays Bioinformatics 2005, 21(14):3105-3113. 15905280
19. Qiu X Brooks AI Klebanov L Yakovlev A The effects of normalization on the correlation structure of microarray data BMC Bioinformatics 2005, 6:120. 1156869 15904488
20. Qiu X Klebanov L Yakovlev A Correlation between gene expression levels and limitations of the empirical bayes methodology for finding differentially expressed genes Statistical Applications in Genetics and Molecular Biology 2005, 4:34.
21. Almudevar A Klebanov LB Qiu X Salzman P Yakovlev AY Utility of correlation measures in analysis of gene expression NeuroRx 2006, 3(3):384-395. 16815221
22. Qiu X Yakovlev A Some comments on instability of false discovery rate estimation J Bioinform Comput Biol 2006, 4(5):1057-1068. 17099941
23. Klebanov L Qiu X Yakovlev A Testing differential expression in non-overlapping gene pairs: A new perspective for the empirical Bayes method Journal of Bioinformatics and Computational Biology 2008, 6:301-316.
24. Klebanov L Yakovlev A Diverse correlation structures in gene expression data and their utility in improving statistical inference Annals of Applied Statistics 2008, 1(2):538-559.
25. Klebanov L Glazko G Salzman P Yakovlev A Xiao Y A multivariate extension of the gene set enrichment analysis J Bioinform Comput Biol 2007, 5(5):1139-1153. 17933015
26. Eisen M Spellman P Brown P Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci U S A 1998, 95(25):14863-14868. 9843981 24541