Calculation of reliable transcript levels of annotated genes on the basis of multiple probe-sets in Affymetrix microarrays

Acta Biochimica Polonica

Volumn 56, Issue 2, 2009, Pages 271-277

  Jaksik, Roman ^a   Polańska, Joanna ^a   Herok, Robert ^b   Rzeszowska Wolny, Joanna ^a,b  

^a SILESIAN UNIVERSITY OF TECHNOLOGY   (Poland)

^b INSTITUTE OF ONCOLOGY   (Poland)

Author keywords

Affymetrix microarrays; Multiple probe sets; NucleoDix computer program; Outlier detection; Transcript profiles

Indexed keywords

EID: 68249092641     PISSN: 0001527X     EISSN: 1734154X     Source Type: Journal    
DOI: 10.18388/abp.2009_2459     Document Type: Article

References (39)

1. Affymetrix (2004) GeneChip Expression Analysis - Technical Manual. pp 185.
2. Bolstad B (2008) RMAExpress. http://rmaexpress.bmbolstad.com/
3. Bourquin J, Subramanian A, Langebrake C, Reinhardt D, Bernard O, Ballerini P, Baruchel A, Cave H, Dastugue N, Hasle H, Kaspers G, Lessard M, Michaux L, Vyas P, Wering E, Zwaan C, Golub T, Orkinar S (2006) Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling. Proc Natl Acad Sci USA 103: 3339-3344.
4. Buck K, Vanek M, Groner B, Ball RK (1992) Multiple forms of prolactin receptor messenger ribonucleic acid are specifically expressed and regulated in murine tissues and the mammary cell line HC11. Endocrinology 130: 1108-1114.
5. Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z (2005) Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 6: 107.
6. Chalifa-Caspi V, Yanai I, Ophir R, Rosen N, Shmoish M, Benjamin-Rodrig H, Shklar M, Stein TI, Shmueli O, Safran M, Lancet D (2004) GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes. Bioinformatics 20: 1457-1458.
7. Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33: e175.
8. Dixon WJ (1953) Processing data for outliers. Biometrics 9: 74-89.
9. Elbez Y, Farkash-Amar S, Simon I (2006) An analysis of intra array repeat: the good, the bad and the noninformative. BMC Genomics 7: 136.
10. Elo LL, Lahti L, Skottman H, Kylaniemi M, Lahesmaa R, Aittokallio T (2005) Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res 33: e193.
11. Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S (2007) Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics 8: 446-452.
12. Gautier L, Møller M, Friis-Hansen L, Knudsen S (2004) Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics 5: 111.
13. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
14. Györffy B, Schäfer R (2008) Meta-analysis of gene expression profiles related to relapse-free survival in 1,079 breast cancer patients. Breast Cancer Res Treat Epub ahead of print.
15. Harbig J, Sprinkle R, Enkemann SA (2005) A sequencebased identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array. Nucleic Acids Res 33: e31.
16. Heydebreck A, Huber W, Gentleman R (2004) Differential Expression with the Bioconductor Project. Bioconductor Project Working Papers Working Paper 7.
17. Hwang KB, Kong SW, Greenberg SA, Park PJ (2004) Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics 5: 159.
18. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
19. Jordan I, Marino-Ramirez L, Koonin E (2005) Evolutionary significance of gene expression divergence. Gene 345: 119-126.
20. Karlsson E, Delle U, Danielsson A, Olsson B, Abel F, Karlsson P, Helou K (2008) Gene expression variation to predict 10-year survival in lymph-node-negative breast cancer. BMC Cancer 8: 254.
21. Kothapalli R, Yoder SJ, Mane S, Loughran TPJ (2002) Microarray results: how accurate are they? BMC Bioinformatics 3: 22.
22. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18: 405-412.
23. Ladd AN, Cooper TA (2002) Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol 3: reviews0008.
24. Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc Natl Acad Sci 98: 31-36.
25. Li H, Zhu D, Cook M (2008) A statistical framework for consolidating "ibling" probe sets for Affymetrix Gene-Chip data. BMC Genomics 9: 188.
26. Liao B, Zhang J (2006) Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 23: 530-540.
27. Lim SJ, Jung HH, Cho YA (2006) Postnatal development of myosin heavy chain isoforms in rat extraocular muscles. Mol Vis 12: 243-250.
28. Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 31: 82-86.
29. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridisation to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680.
30. Lu X, Zhang X (2006) The effect of GeneChip gene definitions on the microarray study of cancers. Bioessays 28: 739-746.
31. Lu J, Lee JC, Salit ML, Cam MC (2007) Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays. BMC Bioinformatics 8: 108.
32. Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z (2004) Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 32: e74.
33. Okoniewski MJ, Miller CJ (2006) Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics 7: 276.
34. Perez-Iratxeta C, Palidwor G, Porter CJ, Sanche NA, Huska MR, Suomela BP, Muro EM, Krzyzanowski PM, Hughes E, Campbell PA, Rudnicki MA, Andrade MA (2005) Study of stem cell function using microarray experiments. FEBS Lett 579: 1795-1801.
35. Ramsay G (1998) DNA chips: state-of-the art. Nat Biotechnol 16: 40-44.
36. Stalteri MA, Harrison AP (2007) Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics 8: 13-27.
37. Stoughton RB (2005) Applications of DNA microarrays in biology. Annu Rev Biochem 74: 53-82.
38. Yu H, Wang F, Tu K, Xie L, Li YY, Li YX (2007) Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. BMC Bioinformatics 8: 194.
39. 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.