Quality assessment of the Affymetrix U133A&B probesets by target sequence mapping and expression data analysis

In Silico Biology

Volumn 7, Issue 3, 2007, Pages 241-260

  Orlov, Yuriy L ^a   Zhou, Jiangtao ^a   Lipovich, Leonard ^a   Shahab, Atif ^b   Kuznetsov, Vladimir A ^a  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b BIOINFORMATICS INSTITUTE   (Singapore)

Author keywords

Breast cancer; Cross hybridization; Gene expression; Human genome; Interspersed repeats; Noise signals; Sense antisense gene pairs; Target sequences; U133 microarray

Indexed keywords

ESTROGEN RECEPTOR BETA; GENOMIC DNA; MESSENGER RNA;

BREAST CANCER; CONFERENCE PAPER; CROSS HYBRIDIZATION; EXPRESSED SEQUENCE TAG; FOOD AND DRUG ADMINISTRATION; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE LOCATION; GENE MAPPING; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; HUMAN; HUMAN GENOME; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; NONHUMAN; QUALITY CONTROL; QUANTITATIVE ANALYSIS; RELIABILITY;

CHROMOSOME MAPPING; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER;

EID: 38949188928     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (25)

1. Chen, J., Sun, M., Kent, W. J., Huang, X., Xie, H., Wang, W., Zhou, G., Shi, R. Z. and Rowley, J. D. (2004). Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res. 32, 4812-4820.
2. Chua, A. L.-S., Ivshina, A. V. and Kuznetsov, V. A. (2006). Pareto-Gamma Statistics reveals global resealing in transcriptomes of low and high aggressive breast cancer phenotypes. In: Pattern Recognition in Bioinformatics (PRIB-2006), Ragapakese, J. C., Wong, L. and Acharya, R. (eds.), LNCS 4146, Springer-Verlag Berlin-Heidelberg, pp.49-59.
3. Dai, M., Wang, P., Boyd, A. D., Kostov, G., Athey, B., Jones, E. G., Bunney, W. E., Myers, R. M., Speed, T. P., Akil, H., Watson, S. J. and Meng, F. (2005). Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 33, e175.
4. Gautier, L., Møller, M., Friis-Hansen, L. and Knudsen, S. (2004). Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics 5, 111.
5. Harbig, J., Sprinkle R. and Enkemann S. A. (2005). A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array. Nucleic Acids Res. 33, e31.
6. Ivshina, A. V., George, J., Senko, O., Mow, B., Putti, T. C., Smeds, J., Nordgren, H., Wong, J. E. L., Liu, E. T., Bergh, J., Kuznetsov, V. A. and Miller, L. D. (2006). Genetic reclassification. of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res. 66, 10292-10301.
7. Katayama, S., et al.; RIKEN Genome Exploration Research Group; Genome Science Group (Genome Network Project Core Group); FANTOM Consortium (2005). Antisense transcription in the mammalian transcriptome. Science 309, 1564-1566.
8. Kuznetsov, V. A., Senkol, O. V, Miller, L. D. and Ivshina, A. V. (2006a). Statistically weighted voting analysis of microarrays for molecular pattern selection and discovery cancer genotypes. Intern. J. Computer Science and Network Security 6(12), 73-82.
9. Kuznetsov, V. A., Zhou, J. T., George, J. and Orlov, Y. L. (2006b). Genome-wide co-expression patterns of human cis-antisense gene pairs. Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure. Novosibirsk, Inst. of Cytology & Genetics vol. 1, pp. 90-93.
10. Leong, H. S., Yates, T., Wilson, C. and Miller, C. J. (2005). ADAPT: A database of affymetrix probesets and transcripts. Bioinformatics 21 2552-2553.
11. Liu, G., Loraine, A. E., Shigeta, R., Cline, M., Cheng, J., Valmeekam V., Sun S., Kulp, D. and Siani-Rose, M. A. (2003). NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 31, 82-86.
12. MAS 5.0 algorithm. Affymetrix. (2002). Statistical Algorithms Description Document. Santa Clara, CA: Affymetrix, Inc. (http://www.affymetrix.com/support/technical/whitepapers/ sadd_whitepaper.pdf)
13. Mecham, B. H., Wetmore, D. Z., Szallasi, Z., Sadovsky, Y., Kohane, I. and Mariani, T. J. (2004). Increased measurement accuracy for sequence-verified microarray probes. Physiol. Genomics 18, 308-315.
14. Miller, L. D., Smeds, J., George, J., Vega, V. B., Vergara, L., Ploner, A., Pawitan, Y., Hall, P., Klaar, S., Liu, E. T. and Bergh, J. (2005). An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc., Natl. Acad. Sci. USA 102, 13550-13555.
15. Okoniewski, M. J. and Miller, C. J. (2006). Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics 7, 276.
16. Orlov, Y. L., Zhou, J. T., Lipovich, L., Yong, H. C., Li, Y., Shahab, A. and Kuznetsov, V. A. (2006). A comprehensive quality assessment of the Affymetrix U133A&B probesets by an integrative genomic and clinical data analysis approach. In: Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure. Novosibirsk, Inst. of Cytology & Genetics, vol. 1, pp. 126-129.
17. Patterson, T. A., Lobenhofer, E. K., Fulmer-Smentek, S. B., Collins, P. J., Chu, T.-M., Bao, W., Fang, H., Kawasaki, E. S., Hager, J., Tikhonova, I. R., Walker, S. J., Zhang, L., Hurban, P., de Longueville, F., Fuscoe, J. C., Tong, W., Shi, L. and Wolfinger, R. D. (2006). Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat. Biotechnol. 24, 1140-1150.
18. Shames, D. S., Girard, L., Gao, B., Sato, M., Lewis, C. M., Shivapurkar, N., Jiang, A., Perou, C. M., Kim, Y. H., Pollack, J. R., Fong, K. M., Lam, C. L., Wong, M., Shyr, Y., Nanda, R., Olopade, O. I., Gerald, W., Euhus, D. M., Shay, J. W., Gazdar, A. F. and Minna, J. D. (2006). A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med. 3, e486.
19. Shi, L., et al.; MAQC Consortium (2006). The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 24, 1151-1161.
20. Stalteri, M. A. and Harrison, A. P. (2007). Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics 15, 8-13.
21. Tusher, V G., Tibshirani, R. and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116-5121.
22. Wu, C., Carta, R. and Zhang, L. (2005). Sequence dependence of cross-hybridization on short oligo microarrays. Nucleic Acids Res. 33 e84.
23. Yelin, R., et al. (2003). Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21, 379-386.
24. Zhang, J., Finney, R. P., Clifford, R. J., Derr, L. K. and Buetow, K. H. (2005). Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach. Genomics 85, 297-308.
25. Zhang, Y., Liu, X. S., Liu, Q. R. and Wei, L. (2006). Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 34, 3465-3475.