Evaluation of gene expression measurements from commercial microarray platforms

Nucleic Acids Research

Volumn 31, Issue 19, 2003, Pages 5676-5684

  Tan, Paul K ^e   Downey, Thomas J ^a   Spitznagel Jr , Edward L ^b   Xu, Pin ^e   Fu, Dadin ^e   Dimitrov, Dimiter S ^c   Lempicki, Richard A ^d   Raaka, Bruce M ^e   Cam, Margaret C ^e  

^a Partek Inc   (United States)

^b WASHINGTON UNIVERSITY   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

^d SAIC FREDERICK INC   (United States)

^e NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; RNA;

ARTICLE; BINDING ASSAY; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; CULTURE MEDIUM; GENE EXPRESSION PROFILING; GENE TARGETING; GENE TECHNOLOGY; HUMAN; HUMAN CELL; MEASUREMENT; PRIORITY JOURNAL; RNA ANALYSIS; RNA HYBRIDIZATION; RNA ISOLATION; SERUM; VALIDATION PROCESS; CELL LINE; COMPARATIVE STUDY; DNA MICROARRAY; EVALUATION; INDUSTRY; REPRODUCIBILITY; STANDARD; STATISTICAL ANALYSIS; STATISTICS;

EUKARYOTA;

CELL LINE; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; INDUSTRY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS;

EID: 0141905890     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg763     Document Type: Article

References (20)

1. Yang,X., Pratley,R.E., Tokraks,S., Bogardus,C. and Permana,P.A. (2002) Microarray profiling of skeletal muscle tissues from equally obese, non-diabetic insulin-sensitive and insulin-resistant Pima Indians. Diabetologia, 45, 1584-1593.
2. Chuaqui,R.F., Bonner,R.F., Best,C.J., Gillespie,J.W., Flaig,M.J., Hewitt,S.M., Phillips,J.L., Krizman,D.B., Tangrea,M.A., Ahram,M., Linehan,W.M., Knezevic,V. and Emmert-Buck,M.R. (2002) Post-analysis follow-up and validation of microarray experiments. Nature Genet., 32, 509-514.
3. Holloway,A.J., Van Laar,R.K., Tothil,R.W. and Bowtell,D.D.L. (2002) Options available-from start to finish-for obtaining data from DNA microarrays II. Nature Genet., 32, 481-489.
4. Edgar,R., Domrachev,M. and Lash,A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
5. Kuo,W.P., Jenssen,T.K., Butte,A.J., Ohno-Machado,L. and Kohane,I.S. (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics, 18, 405-412.
6. Yang,Y.H., Dudoit,S., Luu,P., Lin,D.M., Peng,V., Ngai,J. and Speed,T.P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res., 30, e15.
7. Bouck,J., Yu,W., Gibbs,R. and Worley,K. (1999) Comparison of gene indexing databases. Trends Genet., 15, 159-162.
8. Kerr,M.K., Martin,M. and Churchill,G.A. (2000) Analysis of variance for gene expression microarray data. J. Comput. Biol., 7, 819-837.
9. Wolfinger,R.D., Gibson,G., Wolfinger,E.D., Bennett,L., Hamadeh,H., Bushel,P., Afshari,C. and Paules R.S. (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J. Comput. Biol., 8, 625-637.
10. Churchill,G.A. and Oliver B. (2001) Sex, flies and microarrays. Nature Genet., 29, 355-356.
11. Cheng,L. and Wong,W.H. (2001a) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection, Proc. Natl Acad. Sci. USA, 98, 31-36.
12. Nadon,R. and Shoemaker,J. (2002) Statistical issues with microarrays: processing and analysis. Trends Genet., 18, 265-271.
13. Hosack,D.A., Dennis,G., Sherman,B.T., Lane,H.C. and Lempicki,R.A. (2003) Identifying biological themes within lists of genes with EASE. Genome Biol., 4, in press.
14. Hardikar,A., Raaka,B., Geras-Raaka,E. and Gershengorn,M. (2003) Human pancreatic precursor cells can be induced to differentiate into beta cells, de-differentiate, proliferate and differentiate again. 63rd Scientific Sessions, American Diabetes Association, Diabetes, 52, A43.
15. Kothapalli,R., Yoder,S.J., Mane,S. and Loughran,T.P. (2002) Microarray results: how accurate are they? Bioinformatics, 3, 22.
16. Irizarry,R.A., Bolstad,B.M., Collin,F., Cope,L.M., Hobbs,B. and Speed,T.P. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res., 31, e15.
17. Tanaka,T.S., Jaradat,S.A., Lim,M.K., Kargul,G.J., Wang,X., Grahovac,M.J., Pantano,S., Sano,Y., Piao,Y., Nagaraja,R., Doi,H., Wood,W.H.,III, Becker,K.G. and Ko,M.S. (2000) Genome-wide expression profiling of mid-gestation placenta and embryo using a 15 000 mouse developmental cDNA microarray. Proc. Natl Acad. Sci. USA, 97, 9127-9132.
18. Taniguchi,M., Miura,K., Iwao,H. and Yamanaka,S. (2001) Quantitative assessment of DNA microarrays-comparison with Northern blot analyses. Genomics, 71, 34-39.
19. AlMoustafa,A.E., Alaoui-Jamali,M.A., Batist,G., Hernandez-Perez,M., Serruya,C., Alpert,L., Black,M.J., Sladek,R. and Foulkes,W.D. (2002) Identification of genes associated with head and neck carcinogenesis by cDNA microarray comparison between matched primary normal epithelial and squamous carcinoma cells. Oncogene, 21, 2634-2640.
20. Barczak,A., Rodriguez,M.W., Hanspers,K., Koth,L.L., Tai,Y.C., Bolstad,B.M., Speed,T.P. and Erle,D.J. (2003) Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res., 13, 1775-1785.