Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Wang, Xujing ^a,b   Jia, Shuang ^a,b   Meyer, Lisa ^a,b   Xiang, Bixia ^a,b   Chen, Li Yen ^b   Jiang, Nan ^c   Moreno, Carol ^b   Jacob, Howard J ^b   Ghosh, Soumitra ^a,b   Hessner, Martin J ^a,b  

^a CHILDREN S HOSPITAL OF WISCONSIN   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

^c Roche NimbleGen Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CDNA MICROARRAY TECHNOLOGY; COMPREHENSIVE QUALITIES; DATA PROCESSING PIPELINES; EXPRESSION MEASUREMENTS; GENE EXPRESSION PROFILING; LINEAR RELATIONSHIPS; MICROARRAY TECHNOLOGIES; TECHNICAL ADVANCEMENT;

DATA COMPRESSION RATIO; DATA PROCESSING; GENE EXPRESSION; MICROARRAYS;

QUALITY CONTROL;

COMPLEMENTARY DNA; FLUORESCENT DYE; RNA;

ARTICLE; DNA HYBRIDIZATION; DNA MICROARRAY; DNA PROBE; FILTRATION; GENE EXPRESSION PROFILING; GENETIC HETEROGENEITY; INFORMATION PROCESSING; LINEAR SYSTEM; MOLECULAR CLONING; QUALITY CONTROL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCORING SYSTEM; STATISTICAL SIGNIFICANCE; ANIMAL; CHEMISTRY; GENETICS; LIVER; METABOLISM; PROCEDURES; RAT; REPRODUCIBILITY; STANDARDS;

ANIMALS; FLUORESCENT DYES; GENE EXPRESSION PROFILING; LIVER; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUALITY CONTROL; RATS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA;

EID: 33748657365     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-378     Document Type: Article

References (35)

1. Brown PO, Botstein D: Exploring the new world of the genome with DNA microarrays. Nat Genet 1999, 21 (1 Suppl):33-37.
2. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N: Module networks: identifying, regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34(2):166-176.
3. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L: Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001, 292(5518):929-934.
4. Miklos GL, Maleszka R: Microarray reality checks in the context of a complex disease. Nat Biotechnol 2004, 22(5):615-621.
5. Chuaqui RF, Bonner RF, Best CJ, Gillespie JW, Flaig MJ, Hewitt SM, Phillips JL, Krizman DB, Tangrea MA, Ahram M, Linehan WM, Knezevic V, Emmert-Buck MR: Post-analysis follow-up and validation of microarray experiments. Nat Genet 2002, 32(Suppl):509-514.
6. Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, et al.: Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2005, 2(5):351-356.
7. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W: Multiple-laboratory comparison of microarray platforms. Nat Methods 2005, 2(5):345-350.
8. Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J: Independence and reproducibility across microarray platforms. Nat Methods 2005, 2(5):337-344.
9. Yauk CL, Berndt ML, Williams A, Douglas GR: Comprehensive comparison of six microarray technologies. Nucleic Acids Res 2004, 32(15):e124.
10. Johnson K, Lin S: QA/QC as a pressing need for microarray analysis: meeting report from CAMDA'02. Biotechniques 2003:62-63.
11. Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA: Control of pancreas and liver gene expression by HNF transcription factors. Science 2004, 303(5662):1378-1381.
12. Wang X, Ghosh S, Guo S-W: Quantitative quality control in microarray image processing and data acquisition. Nucleic Acids Research 2001, 29:E75-82.
13. Wang X, Hessner MJ, Wu Y, Pati N, Ghosh S: Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction. Bioinformatics 2003, 19:1341-1347.
14. Yue H, Eastman PS, Wang BB, Minor J, Doctolero MH, Nuttall RL, Stack R, Becker JW, Montgomery JR, Vainer M, Johnston R: An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res 2001, 29(8):E41-41.
15. Hessner MJ, Meyer L, Tackes J, Muheisen S, Wang X: Immobilized support-bound probe and glass surface chemistry as variables in microarray fabrication. BMC Genomics 2004, 5:53.
16. Hessner M, Wang X, Hulse K, Meyer L, Wu Y, Nye S, Guo S-W, Ghosh S: Three color cDNA microarrays: quantitative assessment through the use of Fluorescein-Labeled Probes. Nucl Acids Res 2003, 31:e14.
17. Hessner MJ, Wang X, Khan S, Meyer L, Schlicht M, Tackes J, Datta M, Jacob HJ, Ghosh S: Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. Nucl Acids Res 2003, 31:e60.
18. Wang Y, Wang X, Guo SW, Ghosh S: Conditions to ensure competitive hybridization in two-color microarray: a theoretical and experimental analysis. Biotechniques 2002, 32(6):1342-1346.
19. Wang X, Jiang N, Feng X, Xie Y, Tonellato PJ, Ghosh S, Hessner MJ: A Novel Approach For High Quality Microarray Processing Using Third-Dye Array Visualization Technology. IEEE Trans NanoBioscience 2003, 2(4):193-201.
20. Rajeevan MS, Vernon SD, Taysavang N, Unger ER: Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR. J Mol Diagn 2001, 3(1):26-31.
21. Cleveland WS, Devlin SJ: Locally weighted regression: an approach to regression analysis by local fitting. journal of the American statistical, Association 1988, 83(403):596-610.
22. Bacon D, Watts D: Estimating the transition between two intersecting straight lines. Biometrika 1971, 58:525-535.
23. Colantuoni C, Henry G, Zeger S, Pevsner J: Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatially systematic artifacts. Biotechniques 2002, 32(6):1316-1320.
24. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30(4):e15.
25. Wilson DL, Buckley MJ, Helliwell CA, Wilson IW: New normalization methods for cDNA microarray data. Bioinformatics 2003, 19(11):1325-1332.
26. 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(10):e48.
27. Draghici S, Khatri P, Shah A, Tainsky MA: Assessing the functional bias of commercial microarrays using the onto-compare database. Biotechniques 2003:55-61.
28. Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA: Identifying biological themes within lists of genes with EASE. Genome Biology 2003, 4(6):p4.
29. Wang X, Becker FF, Gascoyne PR: Membrane dielectric changes indicate induced apoptosis in HL-60 cells more sensitively than surface phosphatidylserine expression or DNA fragmentation. Biochim Biophys Acta 2002, 1564(2):412-420.
30. Khatri P, Draghici S: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005.
31. Hessner MJ, Xiang B, Jia S, Geoffrey R, Holmes S, Meyer L, Muheisen S, Wang X: Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms. Physiol Genomics 2006, 25(1):166-178.
32. Hessner MJ, Singh VK, Wang X, Khan K, Tschannen MR, Zahrt TC: Visualization and Quality Control of Spotted 70-mer Arrays Using a Labeled Tracking Oligonucleotide. BMC Genomics 2004, 5:12.
33. Sanchez-Margalet V, Lucas M, Solano F, Goberna R: Sensitivity of insulin-secreting RIN m5F cells to undergoing apoptosis by the protein kinase C inhibitor staurosporine. Exp Cell Res 1993, 209(1):160-163.
34. Hessner M, Wang X, Meyer L, Geoffrey R, Jia S, Fuller J, Lernmark A, Ghosh S: Involvement of eotaxin, eosinophils, and pancreatic predisposition in development of type 1 diabetes mellitus in the BioBressding rat. journal of Immunology 2004, 173(11):6993-7002.
35. Pfaffl MW: A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001, 29(9):e45.