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Issue No.01 - January-February (2011 vol.8)
pp: 217-225
Leo Lahti , Helsinki University of Technology, TKK
Laura L. Elo , University of Turku, Turku
Tero Aittokallio , University of Turku, Turku
Samuel Kaski , Helsinki University of Technology, TKK
Probe defects are a major source of noise in gene expression studies. While existing approaches detect noisy probes based on external information such as genomic alignments, we introduce and validate a targeted probabilistic method for analyzing probe reliability directly from expression data and independently of the noise source. This provides insights into the various sources of probe-level noise and gives tools to guide probe design.
Applications, biology and genetics, parameter learning, probabilistic algorithms.
Leo Lahti, Laura L. Elo, Tero Aittokallio, Samuel Kaski, "Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no. 1, pp. 217-225, January-February 2011, doi:10.1109/TCBB.2009.38
[1] C. Benedict, M. Geisler, J. Trygg, N. Huner, and V. Hurry, "Consensus by Democracy. Using Meta-Analyses of Microarray and Genomic Data to Model the Cold Acclimation Signaling Pathway in Arabidopsis," Plant Physiology, vol. 141, no. 4, pp. 1219-1232, 2006.
[2] Z. Hu, C. Fan, D.S. Oh, J. Marron, X. He, B.F. Qaqish, C. Livasy, L.A. Carey, E. Reynolds, L. Dressler, A. Nobel, J. Parker, M.G. Ewend, L.R. Sawyer, J. Wu, Y. Liu, R. Nanda, M. Tretiakova, A.R. Orrico, D. Dreher, J.P. Palazzo, L. Perreard, E. Nelson, M. Mone, H. Hansen, M. Mullins, J.F. Quackenbush, M.J. Ellis, O.I. Olopade, P.S. Bernard, and C.M. Perou, "The Molecular Portraits of Breast Tumors are Conserved Across Microarray Platforms," BMC Genomics, vol. 7, p. 96, 2006.
[3] S. Katz, R.A. Irizarry, X. Lin, M. Tripputi, and M.W. Porter, "A Summarization Approach for Affymetrix GeneChip Data Using a Reference Training Set from a Large, Biologically Diverse Database," BMC Bioinformatics, vol. 7, p. 464, 2006.
[4] S. Yoon, Y. Yang, J. Choi, and J. Seong, "Large Scale Data Mining Approach for Gene-Specific Standardization of Microarray Gene Expression Data," Bioinformatics, vol. 22, pp. 2898-2904, 2006.
[5] D. Lockhart, H. Dong, M. Byrne, M. Follettie, M. Gallo, M. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E. Brown, "Expression Monitoring by Hybridization to High-Density Oligonucleotide Arrays," Nature Biotechnology vol. 14, pp. 1675-80, 1996.
[6] R.A. Irizarry, D. Warren, F. Spencer, I.F. Kim, S. Biswal, B.C. Frank, E. Gabrielson, J.G.N. Garcia, J. Geoghegan, G. Germino, C. Griffin, S.C. Hilmer, E. Hoffman, A.E. Jedlicka, E. Kawasaki, F. Martinez-Murillo, L. Morsberger, H. Lee, D. Petersen, J. Quackenbush, A. Scott, M. Wilson, Y. Yang, S.Q. Ye, and W. Yu, "Multiple-Laboratory Comparison of Microarray Platforms," Nature Methods, vol. 2, pp. 345-350, 2005.
[7] L. Gautier, M. Moller, L. Friis-Hansen, and S. Knudsen, "Alternative Mapping of Probes to Genes for Affymetrix Chips," BMC Bioinformatics, vol. 5, p. 111, 2004.
[8] K.-B. Hwang, S.W. Kong, S.A. Greenberg, and P.J. Park, "Combining Gene Expression Data from Different Generations of Oligonucleotide Arrays," BMC Bioinformatics, vol. 5, p. 159, 2004.
[9] B.H. Mecham, D.Z. Wetmore, Z. Szallasi, Y. Sadovsky, I. Kohane, and T.J. Mariani, "Increased Measurement Accuracy for Sequence-Verified Microarray Probes," Physiological Genomics, vol. 18, pp. 308-315, 2004.
[10] M. Dai, P. Wang, A.D. Boyd, G. Kostov, B. Athey, E.G. Jones, W.E. Bunney, R.M. Myers, T.P. Speed, H. Akil, S.J. Watson, and F. Meng, "Evolving Gene/Transcript Definitions Significantly Alter the Interpretation of Genechip Data," Nucleic Acids Research, vol. 33, p. e175, 2005.
[11] J. Zhang, R.P. Finney, R.J. Clifford, L.K. Derr, and K.H. Buetow, "Detecting False Expression Signals in High-Density Oligonucleotide Arrays by an In Silico Approach," Genomics, vol. 85, pp. 297-308, 2005.
[12] MAQC Consortium, "The Microarray Quality Control (MAQC) Project Shows Inter- and Intraplatform Reproducibility of Gene Expression Measurements," Nature Biotechnology, vol. 24, pp. 1151-1161, 2006.
[13] Y. Tu, G. Stolovitzky, and U. Klein, "Quantitative Noise Analysis for Gene Expression Microarray Experiments," Proc. Nat'l Academy of Sciences USA, vol. 99, pp. 14031-14036, 2002.
[14] C. Li and W.H. Wong, "Model-Based Analysis of Oligonucleotide Arrays: Expression Index Computation and Outlier Detection," Proc. Nat'l Academy of Sciences USA, vol. 98, pp. 31-36, 2001.
[15] R.A. Irizarry, B.M. Bolstad, F. Collin, L.M. Cope, B. Hobbs, and T.P. Speed, "Summaries of Affymetrix GeneChip Probe Level Data," Nucleic Acids Research, vol. 31, p. e15, 2003.
[16] Z. Wu and R. Irizarry, "Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays," Proc. Eight Conf. Research in Computational Molecular Biology (RECOMB '04), pp. 98-106, 2004.
[17] S. Hochreiter, D.-A. Clevert, and K. Obermayer, "A New Summarization Method for Affymetrix Probe Level Data," Bioinformatics, vol. 22, pp. 943-949, 2006.
[18] M. Milo, A. Fazeli, M. Niranjan, and N. Lawrence, "A Probabilistic Model for the Extraction of Expression Levels from Oligonucleotide Arrays," Biochemical Soc. Trans., vol. 31, pp. 1510-1512, 2003.
[19] A.-M.K. Hein, S. Richardson, H.C. Causton, G.K. Ambler, and P.J. Green, "BGX: A Fully Bayesian Integrated Approach to the Analysis of Affymetrix GeneChip Data," Biostatistics, vol. 6, pp. 349-373, 2005.
[20] X. Li, Z. He, and J. Zhou, "Selection of Optimal Oligonucleotide Probes for Microarrays Using Multiple Criteria, Global Alignment and Parameter Estimation," Nucleic Acids Research, vol. 33, pp. 6114-6123, 2005.
[21] R. Mei, E. Hubbell, S. Bekiranov, M. Mittmann, F.C. Christians, M.-M. Shen, G. Lu, J. Fang, W.-M. Liu, T. Ryder, P. Kaplan, D. Kulp, and T.A. Webster, "Probe Selection for High-Density Oligonucleotide Arrays," Proc. Nat'l Academy of Sciences USA, vol. 100, pp. 11237-11242, 2003.
[22] F. Naef and M.O. Magnasco, "Solving the Riddle of the Bright Mismatches: Labeling and Effective Binding in Oligonucleotide Arrays," Physical Rev. E, vol. 68, 2003.
[23] C. Wu, R. Carta, and L. Zhang, "Sequence Dependence of Cross-Hybridization on Short Oligo Microarrays," Nucleic Acids Research, vol. 33, p. e84, 2005.
[24] A.L. Oberg, D.W. Mahoney, K.V. Ballman, and T.M. Therneau, "Joint Estimation of Calibration and Expression for High-Density Oligonucleotide Arrays," Bioinformatics, vol. 22, pp. 2381-2387, 2006.
[25] L. Zhang, L. Wang, A. Ravindranathan, and M. Miles, "A New Algorithm for Analysis of Oligonucleotide Arrays: Application to Expression Profiling in Mouse Brain Regions," J. Molecular Biology, vol. 317, pp. 225-235, 2002.
[26] L.L. Elo, L. Lahti, H. Skottman, M. Kyläniemi, R. Lahesmaa, and T. Aittokallio, "Integrating Probe-Level Expression Changes Across Generations of Affymetrix Arrays," Nucleic Acids Research, vol. 33, p. e193, 2005.
[27] M.E. Ross, X. Zhou, G. Song, S. Shurtleff, K. Girtman, W. Williams, H.-C. Liu, R. Mahfouz, S. Raimondi, N. Lenny, A. Patel, and J. Downing, "Classification of Pediatric Acute Lymphoblastic Leukemia by Gene Expression Profiling," Blood, vol. 102, pp. 2951-2959, 2003.
[28] A.I. Su, M.P. Cooke, K.A. Ching, Y. Hakak, J.R. Walker, T. Wiltshire, A.P. Orth, R.G. Vega, L.M. Sapinoso, A. Moqrich, A. Patapoutian, G.M. Hampton, P.G. Schultz, and J.B. Hogenesch, "Large-Scale Analysis of the Human and Mouse Transcriptomes," Proc. Nat'l Academy of Sciences USA, vol. 99, pp. 4465-4470, 2002.
[29] A.I. Su, T. Wiltshire, S. Batalov, H. Lapp, K.A. Ching, D. Block, J. Zhang, R. Soden, M. Hayakawa, G. Kreiman, M.P. Cooke, J.R. Walker, and J.B. Hogenesch, "A Gene Atlas of the Mouse and Human Protein-Encoding Transcriptomes," Proc. Nat'l Academy of Sciences USA, vol. 101, pp. 6062-6067, 2004.
[30] E.-J. Yeoh et al., "Classification, Subtype Discovery, and Prediction of Outcome in Pediatric Acute Lymphoblastic Leukemia by Gene Expression Profiling," Cancer Cell, vol. 1, pp. 133-143, 2002.
[31] H. Yu, F. Wang, K. Tu, L. Xie, Y. Li, and Y. Li, "Transcript-Level Annotation of Affymetrix Probesets Improves the Interpretation of Gene Expression Data," BMC Bioinformatics, vol. 8, p. e194, 2007.
[32] H. Auer, S. Lyianarachchi, D. Newsom, M.I. Klisovic, G. Marcucci, and K. Kornacker, "Chipping Away at the Chip Bias: RNA Degradation in Microarray Analysis," Nature Genetics, vol. 35, pp. 292-293, 2003.
[33] L. Gautier, L. Cope, B.M. Bolstad, and R.A. Irizarry, "Affy-Analysis of Affymetrix Genechip Data at the Probe Level," Bioinformatics, vol. 20, pp. 307-315, 2004.
[34] C.J. Burden, Y. Pittelkow, and S.R. Wilson, "Adsorption Models of Hybridization and Post-Hybridization Behavior on Oligonucleotide Microarrays," J. Physics: Condensed Matter, vol. 18, pp. 5545-5565, 2006.
[35] A. Sequeira, F. Meng, B. Rollins, R. Myers, E. Jones, S. Watson, H. Akil, A. Schatzberg, J. Barchas, and W. Bunney, V. M.P., "Coding SNPs Included in Exon Arrays for the Study of Psychiatric Disorders," Molecular Psychiatry, vol. 13, pp. 363-365, 2008.
[36] E. Sliwerska, F. Meng, T. Speed, E. Jones, W. Bunney, H. Akil, S. Watson, and M. Burmeister, "SNPs on Chips: The Hidden Genetic Code in Expression Arrays," Biological Psychiatry, vol. 61, pp. 13-16, 2007.
[37] I. Lee, A.A. Dombkowski, and B.D. Athey, "Guidelines for Incorporating Non-Perfectly Matched Oligonucleotides into Target-Specific Hybridization Probes for a DNA Microarray," Nucleic Acids Research, vol. 32, pp. 681-690, 2004.
[38] L.L. Elo, M. Katajamaa, R. Lund, M. Oresic, R. Lahesmaa, and T. Aittokallio, "Improving Identification of Differentially Expressed Genes by Integrative Analysis of Affymetrix and Illumina Arrays," OMICS: A J. Integrative Biology, vol. 10, pp. 369-380, 2006.
[39] A. Gelman, J.B. Carlin, H.S. Stern, and D.B. Rubin, Bayesian Data Analysis, second ed. Chapman & Hall/CRC, 2003.
[40] D. Goldfarb, "A Family of Variable-Metric Methods Derived by Variational Means," Math. of Computation, vol. 24, pp. 23-26, 1970.
[41] M. McGee and Z. Chen, "New Spiked-In Probe Sets for the Affymetrix HG-U133A Latin Square Experiment," COBRA Preprint Series, Article 5, 2006.
[42] R.C. Gentleman, V.J. Carey, D.M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F.L.C. Li, M. Maechler, A.J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J.Y.H. Yang, and J. Zhang, "Bioconductor: Open Software Development for Computational Biology and Bioinformatics," Genome Biology, vol. 5, p. R80, 2004.
[43] D.L. Wheeler, T. Barrett, D.A. Benson, S.H. Bryant, K. Canese, V. Chetvernin, D.M. Church, M. DiCuccio, R. Edgar, S. Federhen, M. Feolo, L.Y. Geer, W. Helmberg, Y. Kapustin, O. Khovayko, D. Landsman, D.J. Lipman, T.L. Madden, D.R. Maglott, V. Miller, J. Ostell, K.D. Pruitt, G.D. Schuler, M. Shumway, E. Sequeira, S.T. Sherry, K. Sirotkin, A. Souvorov, G. Starchenko, R.L. Tatusov, T.A. Tatusova, L. Wagner, and E. Yaschenko, "Database Resources of the National Center for Biotechnology Information," Nucleic Acids Research, vol. 36, suppl. 1, pp. D13-D21, 2008.
[44] W.J. Kent, "BLAT-The BLAST-Like Alignment Tool," Genome Research, vol. 12, pp. 656-664, 2002.
[45] E.C. Rouchka, A.W. Phatak, and A.V. Singh, "Effect of Single Nucleotide Polymorphisms on Affymetrix Match-Mismatch Probe Pairs," Bioinformation, vol. 2, pp. 405-411, 2008.
[46] R.A. Irizarry, B. Hobbs, F. Collin, Y.D. Beazer-Barclay, K.J. Antonellis, U. Scherf, and T.P. Speed, "Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data," Biostatistics, vol. 4, pp. 249-264, 2003.
[47] Y. Xing, K. Kapur, and W.H. Wong, "Probe Selection and Expression Index Computation of Affymetrix Exon Arrays," PLoS ONE, vol. 1, p. e88, 2006.
[48] J. Yan and T.G. Marr, "Computational Analysis of 3-Ends of ESTs Shows Four Classes of Alternative Polyadenylation in Human, Mouse, and Rat," Genome Research, vol. 15, pp. 369-375, 2005.
[49] A. Reverter, W. Barris, S. McWilliam, K. Byrne, Y. Wang, S. Tan, N. Hudson, and B. Dalrymple, "Validation of Alternative Methods of Data Normalization in Gene Co-Expression Studies," Bioinformatics, vol. 21, pp. 1112-1120, 2005.
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