Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Carter, Scott L ^a   Eklund, Aron C ^b   Mecham, Brigham H ^a   Kohane, Isaac S ^a   Szallasi, Zoltan ^a  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CDNA MICROARRAYS; EXPRESSION MEASUREMENTS; GENE EXPRESSION DATA; GENE EXPRESSION MICROARRAY; GENE EXPRESSION PROFILES; HIER-ARCHICAL CLUSTERING; INTEGRATED ANALYSIS; SEQUENCE MATCHING;

CELL CULTURE; CLONING; DISEASES; GENE EXPRESSION; MICROARRAYS;

PROBES;

COMPLEMENTARY DNA; DNA PROBE; RNA;

ARTICLE; BREAST CANCER; CANCER CLASSIFICATION; CELL LINE; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CORRELATION; HUMAN; MOLECULAR PROBE; BIOLOGY; BREAST TUMOR; CHEMISTRY; CLUSTER ANALYSIS; DNA PROBE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; LUNG TUMOR; METABOLISM; NEOPLASM; PATHOLOGY; PHYLOGENY; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS; TUMOR CELL LINE;

BREAST NEOPLASMS; CELL LINE, TUMOR; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; DNA PROBES; DNA, COMPLEMENTARY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LUNG NEOPLASMS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; REPRODUCIBILITY OF RESULTS; RNA; RNA, NEOPLASM; SENSITIVITY AND SPECIFICITY;

EID: 25444515422     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-107     Document Type: Article

References (24)

1. Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lonning P, Borresen-Dale AL: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001, 98:10869-10874.
2. Lossos IS, Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, Levy R: Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med 2004, 350:1828-1837.
3. Watson A, Mazumder A, Stewart M, Balasubramanian S: Technology for microarray analysis of gene expression. Curr Opin Biotechnol 1998, 9:609-614.
4. Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z: Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Research 2004, 32:e74.
5. Boyd MR, Paull KD: Some practical considerations and applications of the National Cancer Institute in vitro anticancer drug discovery screen. Drug Dev Res 1995, 34:91-109.
6. West M, Blanchette C, Dressman H, Huang E, Ishida S, Spang R, Zuzan H, Olson JA Jr, Marks JR, Nevins JR: Predicting the clinical status of human breast cancer by using gene expression profiles. Proc Natl Acad Sci USA 2001, 98:11462-11467.
7. Sørlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lonning PE, Brown PO, Borresen-Dale AL, Botstein D: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 2003, 100:8418-8423.
8. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31:e15.
9. Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, Horng CF, Bild A, Iversen ES, Liao M, Chen CM, West M, Nevins JR, Huang AT: Gene expression predictors of breast cancer outcomes. Lancet 2003, 361:1590-1596.
10. Signoretti S, Marcotullio L, Richardson A, Ramaswamy S, Isaac B, Rue M, Monti F, Loda M, Pagano M: Oncogenic role of the ubiquitin ligase subunit Skp2 in human breast cancer. The Journal of Clinical Investigation 2002, 110:633-641.
11. Garber M, Troyanskaya OG, Schluens K, Peterson S, Thaesler Z, Oacyna-Genglebach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Peterson I: Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA 2001, 98:13784-13789.
12. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillete M, Loda M, Weber G, Sugarbaker D, Meyerson M: Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 2001, 98:13790-13795.
13. Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC: Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003, 31:5676-5684.
14. Gold D, Coombes K, Medhane D, Ramaswamy A, Ju Z, Strong L, Koo JS, Kapoor M.: A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays. BMC Genomics 2004, 5(1):2.
15. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC: Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res 2002, 30:e48.
16. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS.: Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 2002, 18:405-412.
17. Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS: Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics 2003:27.
18. Lee JK, Bussey KJ, Gwadry FG, Reinhold W, Riddick G, Pelletier SL, Nishizuka S, Szakacs G, Anneraeu J, Shankavavaram U, Lababidi S, Smith LH, Gottesman MM, Weinstein JN: Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biology 2003, 4:R82.
19. Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN: A gene expression database for the molecular pharmacology of cancer. Nat Genet 2000, 24:236-244.
20. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR: Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci USA 2001, 98:10787-10792.
21. Gautier L, Moller M, Friis-Hansen L, Knudsen S: Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics 2004, 5(1):111.
22. 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: Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 2004, 5:R80.
23. Boguski MS, Lowe TM, Tolstoshev CM: dbEST - database for "expressed sequence tags". Nat Genet 1993, 4:332-333.
24. Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jefferey SS, Rees CA, Pollack JR, Ross DT, Johnson H, Akslen LA, Fluge Ø, Pergamenschikov A, Williams C, Zhu SX, Lønning PE, Børresen-Dale A, Brown PO, Botstein D: Molecular portraits of human breast tumors. Nature 2000, 406:747-752.