Autocorrelation analysis reveals widespread spatial biases in microarray experiments

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Koren, Amnon ^a   Tirosh, Itay ^a   Barkai, Naama ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANEUPLOIDY; ARTICLE; CHROMOSOME ANALYSIS; CHROMOSOME IDENTIFICATION; CHROMOSOME POSITIONING; COMPUTER SIMULATION; CONTROLLED STUDY; DNA MICROARRAY; EXPERIMENTAL DESIGN; GENE EXPRESSION; GENETIC DATABASE; MOLECULAR HYBRIDIZATION; NONHUMAN; QUALITY CONTROL; SACCHAROMYCES CEREVISIAE; SPATIAL AUTOCORRELATION ANALYSIS; STATISTICAL ANALYSIS; YEAST; DIAGNOSTIC ERROR; DNA PROBE; METHODOLOGY; REPRODUCIBILITY; RESEARCH; STANDARD;

DIAGNOSTIC ERRORS; DNA PROBES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RESEARCH; YEASTS;

EID: 34447296700     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-164     Document Type: Article

References (47)

1. Eads B Cash A Bogart K Costello J Andrews J Troubleshooting Microarray Hybridizations Methods in Enzymology 2006 411 34-49 16939784
2. Quackenbush J Microarray data normalization and transformation Nat Genet 2002 32 Suppl 496-501 10.1038/ng1032 12454644
3. Tseng GC Oh MK Rohlin L Liao JC Wong WH Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects Nucl Acids Res 2001 29 2549-2557 55725 11410663 10.1093/nar/29.12.2549
4. 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 Nucl Acids Res 2002 30 e15 100354 11842121 10.1093/nar/30.4.e15
5. Grunenfelder B Winzeler EA Treasures and traps in genome-wide data sets: case examples from yeast Nat Rev Genet 2002 3 653-661 10.1038/nrg886 12209140
6. 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 Nucl Acids Res 2003 31 5676-5684 206463 14500831 10.1093/nar/gkg763
7. Miklos GLG Maleszka R Microarray reality checks in the context of a complex disease Nat Biotech 2004 22 615-621 10.1038/nbt965
8. Marshall E Getting the Noise Out of Gene Arrays Science 2004 306 630-631 10.1126/science.306.5696.630 15499004
9. Steinmetz LM Davis RW Maximizing the potential of functional genomics Nat Rev Genet 2004 5 190-201 10.1038/nrg1293 14970821
10. Frantz S An array of problems Nat Rev Drug Discov 2005 4 362-363 10.1038/ nrd1746 15902768
11. Michiels S Koscielny S Hill C Prediction of cancer outcome with microarrays: A multiple random validation strategy The Lancet 2005 365 488-492 10.1016/S0140-6736(05)17866-0
12. Tibshirani R Hong WJ Warnke R Chu G Staudt LM Wright G Dave S Immune Signatures in Follicular Lymphoma N Engl J Med 2005 352 1496-1497 10.1056/NEJM200504073521422 15814892
13. Ein-Dor L Zuk O Domany E Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer PNAS 2006 103 5923-5928 1458674 16585533 10.1073/pnas.0601231103
14. Petersen D Chandramouli GV Geoghegan J Hilburn J Paarlberg J Kim CH Munroe D Gangi L Han J Puri R Staudt L Weinstein J Barrett JC Green J Kawasaki ES Three microarray platforms: An analysis of their concordance in profiling gene expression BMC Genomics 2005 6 63 1140753 15876355 10.1186/1471-2164-6-63
15. Dobbin KK Beer DG Meyerson M Yeatman TJ Gerald WL Jacobson JW Conley B Buetow KH Heiskanen M Simon RM Minna JD Girard L Misek DE Taylor JMG Hanash S Naoki K Hayes DN Ladd-Acosta C Enkemann SA Viale A Giordano TJ Interlaboratory Comparability Study of Cancer Gene Expression Analysis Using Oligonucleotide Microarrays Clin Cancer Res 2005 11 565-572 15701842
16. Irizarry RA Warren D Spencer F Kim IF Biswal S Frank BC Gabrielson E Garcia JGN 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 2 345-350 10.1038/ nmeth756 15846361
17. Larkin JE Frank BC Gavras H Sultana R Quackenbush J Independence and reproducibility across microarray platforms Nat Methods 2005 2 337-344 10.1038/nmeth757 15846360
18. Kuo WP Liu F Trimarchi J Punzo C Lombardi M Sarang J Whipple ME Maysuria M Serikawa K Lee SY McCrann D Kang J Shearstone JR Burke J Park DJ Wang X Rector TL Ricciardi-Castagnoli P Perrin S Choi S Bumgarner R Kim JH Short GF 3rd Freeman MW Seed B Jensen R Church GM Hovig E Cepko CL Park P Ohno-Machado L Jenssen TK A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies Nat Biotechnol 2006 24 832-840 10.1038/nbt1217 16823376
19. Shi L Reid LH Jones WD MAQCconsortium The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat Biotechnol 2006 24 1151-1161 10.1038/nbt1239 16964229
20. Canales RD Luo Y Willey JC Austermiller B Barbacioru CC Boysen C Hunkapiller K Jensen RV Knight CR Lee KY Ma Y Maqsodi B Papallo A Peters EH Poulter K Ruppel PL Samaha RR Shi L Yang W Zhang L Goodsaid FM Evaluation of DNA microarray results with quantitative gene expression platforms Nat Biotech 2006 24 1115-1122 10.1038/nbt1236
21. Kluger Y Yu H Qian J Gerstein M Relationship between gene co-expression and probe localization on microarray slides BMC Genomics 2003 4 49 317287 14667251 10.1186/1471-2164-4-49
22. Balazsi G Kay KA Barabasi AL Oltvai ZN Spurious spatial periodicity of co-expression in microarray data due to printing design Nucl Acids Res 2003 31 4425-4433 169875 12888502 10.1093/nar/gkg485
23. Yu H Nguyen K Royce T Qian J Nelson K Snyder M Gerstein M Positional artifacts in microarrays: Experimental verification and construction of COP, an automated detection tool Nucl Acids Res 2006 gkl871
24. Cho RJ Campbell MJ Winzeler EA Steinmetz L Conway A Wodicka L Wolfsberg TG Gabrielian AE Landsman D Lockhart DJ Davis RW A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle Molecular Cell 1998 2 65-73 10.1016/S1097-2765(00)80114-8 9702192
25. Cohen BA Mitra RD Hughes JD Church GM A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression Nat Genet 2000 26 183-186 10.1038/79896 11017073
26. Gottman JM Time-series analysis: A comprehensive introduction for social scientists New York: Cambridge University Press; 1981
27. Spellman PT Sherlock G Zhang MQ Iyer VR Anders K Eisen MB Brown PO Botstein D Futcher B Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization Mol Biol Cell 1998 9 3273-3297 25624 9843569
28. Futschik ME Crompton T OLIN: Optimized normalization, visualization and quality testing of two-channel microarray data Bioinformatics 2005 21 1724-1726 10.1093/bioinformatics/bti199 15585527
29. Neuvial P Hupe P Brito I Liva S Manie E Brennetot C Radvanyi F Aurias A Barillot E Spatial normalization of array-CGH data BMC Bioinformatics 2006 7 264 1523216 16716215 10.1186/1471-2105-7-264
30. Reimers M Weinstein JN Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases BMC Bioinformatics 2005 6 166 1189079 15992406 10.1186/1471-2105-6-166
31. Bioconductor http://www.bioconductor.org
32. Hughes TR Roberts CJ Dai H Jones AR Meyer MR Slade D Burchard J Dow S Ward TR Kidd MJ Friend SH Marton MJ Widespread aneuploidy revealed by DNA microarray expression profiling Nat Genet 2000 25 333-337 10.1038/ 77116 10888885
33. Hughes TR Marton MJ Jones AR Roberts CJ Stoughton R Armour CD Bennett HA Coffey E Dai H He YD Functional Discovery via a Compendium of Expression Profiles Cell 2000 102 109-126 10.1016/S0092-8674(00)00015-5 10929718
34. Tirosh I Weinberger A Carmi M Barkai N A genetic signature of interspecies variations in gene expression Nat Genet 2006 38 830-834 10.1038/ng1819 16783381
35. Naama Barkai lab Autocorrelations http://barkai-serv.weizmann.ac.il/ autocorrelations/
36. Ihmels J Friedlander G Bergmann S Sarig O Ziv Y Barkai N Revealing modular organization in the yeast transcriptional network Nat Genet 2002 31 370-377 12134151
37. Naama Barkai lab Modules http://www.weizmann.ac.il/home/jan/NG/ MainFrames.html
38. Stanford Microarray Database http://genome-www5.stanford.edu/
39. Sherlock G Hernandez-Boussard T Kasarskis A Binkley G Matese JC Dwight SS Kaloper M Weng S Jin H Ball CA Eisen MB Spellman PT Brown PO Botstein D Cherry JM The Stanford Microarray Database Nucl Acids Res 2001 29 152-155 29818 11125075 10.1093/nar/29.1.152
40. Lee TI Rinaldi NJ Robert F Odom DT Bar-Joseph Z Gerber GK Hannett NM Harbison CT Thompson CM Simon I Zeitlinger J Jennings EG Murray HL Gordon DB Ren B Wyrick JJ Tagne JB Volkert TL Fraenkel E Gifford DK Young RA Transcriptional Regulatory Networks in Saccharomyces cerevisiae Science 2002 298 799-804 10.1126/science.1075090 12399584
41. Marton MJ DeRisi JL Bennett HA Iyer VR Meyer MR Roberts CJ Stoughton R Burchard J Slade D Dai H Bassett DE Hartwell LH Brown PO Friend SH Drug target validation and identification of secondary drug target effects using DNA microarrays Nat Med 1998 4 1293-1301 10.1038/3282 9809554
42. Roberts CJ Nelson B Marton MJ Stoughton R Meyer MR Bennett HA He YD Dai H Walker WL Hughes TR Tyers M Boone C Friend SH Signaling and Circuitry of Multiple MAPK Pathways Revealed by a Matrix of Global Gene Expression Profiles Science 2000 287 873-880 10.1126/science.287.5454.873 10657304
43. Saccharomyces Genome Database http://www.yeastgenome.org/
44. Hardwick JS Kuruvilla FG Tong JK Shamji AF Schreiber SL Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins PNAS 1999 96 14866-14870 24739 10611304 10.1073/pnas.96.26.14866
45. Posas F Chambers JR Heyman JA Hoeffler JP de Nadal E Arino J The Transcriptional Response of Yeast to Saline Stress J Biol Chem 2000 275 17249-17255 10.1074/jbc.M910016199 10748181
46. Dunham MJ Badrane H Ferea T Adams J Brown PO Rosenzweig F Botstein D Characteristic genome rearrangements in experimental evolution of Saccharomycescerevisiae PNAS 2002 99 16144-16149 138579 12446845 10.1073/ pnas.242624799
47. Dunn B Levine RP Sherlock G Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures BMC Genomics 2005 6 53 1097725 15833139 10.1186/1471-2164-6-53