The effect of GeneChip gene definitions on the microarray study of cancers

BioEssays

Volumn 28, Issue 7, 2006, Pages 739-746

  Lu, Xuesong ^a   Zhang, Xuegong ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CANCER; CLUSTER ANALYSIS; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC ANALYSIS; GENETIC DATABASE; HUMAN; INFORMATION PROCESSING; MICROARRAY ANALYSIS; MICROCHIP ANALYSIS; REVIEW;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HUMANS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 33747520366     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.20433     Document Type: Review

References (22)

1. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, et al. 1999. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286:531-537.
2. Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, et al. 1999. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96:6745-6750.
3. Dhanasekaran SM, Barrette TR, Ghosh D, Shah R, Varambally S, et al. 2001. Delineation of prognostic biomarkers in prostate cancer. Nature 412:822-826.
4. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, et al. 2001. Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA 98:13784-13789.
5. Welsh JB, Zarrinkar PP, Sapinoso LM, Kern SG, Behling CA, et al. 2001. Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. Proc Natl Acad Sci USA 98:1176-1181.
6. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AAM, et al. 2002. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530-536.
7. Chen X, Cheng ST, So SK, Fang ST, Barry C, et al. 2002. Gene expression patterns in human liver cancers. Mol Biol Cell 13:1929-1939.
8. Dyrskjot L, Thykjaer T, Kruhoffer M, Jensen JL, Marcussen N, et al. 2003. Identifying distinct classes of bladder carcinoma using microarrays. Nature Genet 33:90-96.
9. Ramaswamy S, Ross KN, Lander ES, Golub TR. 2003. A molecular signature of metastasis in primary solid tumors. Nat Genet 33:49-54.
10. Dave SS, Wright G, Tan B, Rosenwald A, Gascoyne RD, et al. 2004. Prediction of survival in follicular lymphoma based on molecular features of tumor-infiltrating immune cells. N Engl J Med 351:2159-2169.
11. Mecham BH, Wetmore DZ, Szallasi Z, Sadovsky Y, Kohane I, et al. 2004. Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics 18:308-315.
12. Gautier L, Moller M, Friis-Hansen L, Knudsen S. 2004. Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics 5:111-117.
13. Zhang J, Finney RP, Clifford RJ, Derr LK, Buetow KH. 2005. Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach. Genomics 85:297-308.
14. Harbig J, Sprinkle R, Enkemann SA. 2005. A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array. Nucleic Acids Res 33:e31.
15. Dai M, Wang P, Boyd AD, Kostov G, Athey B, et al. 2005. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33:e175.
16. Valmeekam V, Loh YL, San Francisco MJ. 2001. Control of exuT activity for galacturonate transport by the negative regulator ExuR in Erwinia chrysanthemi EC16. Mol Plant Microbe Interact 14:816-820.
17. Li C, Wong WH. 2001. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36.
18. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289-300.
19. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang C-H, et al. 2001. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 98:15149-15154.
20. Zhang X, Lu X, Shi Q, Leung HE, Harris LN, et al. 2006. Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics 7:197.
21. Collobert R, Bengio S. 2001. SVMTorch: Support Vector Machines for Large-Scale Regression Problems. J of Machine Learning Res 1:143-160.
22. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. 2005. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102(43):15545-15550.