Microarrays, deep sequencing and the true measure of the transcriptome

BMC Biology

Volumn 9, Issue , 2011, Pages

  Malone, John H ^a   Oliver, Brian ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; DNA MICROARRAY; DROSOPHILA; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY; REVIEW; SEQUENCE ANALYSIS;

ANIMALS; DROSOPHILA; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, RNA;

EID: 79957665988     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-9-34     Document Type: Review

References (51)

1. Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM, Cook BP, Dufault MR, Ferguson AT, Gao Y, He TC, Hermeking H, Hiraldo SK, Hwang PM, Lopez MA, Luderer HF, Mathews B, Petroziello JM, Polyak J, Zawel L, Zhang W, Zhang X, Zhou W, Haluska FG, Jen J, Sukumar S, et al. Analysis of human transcriptomes. Nat Genet 1999, 23:387-388.
2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Miklos GLG, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, et al. The sequence of the human genome. Science 2001, 291:1304-1351.
3. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
4. Kai T, Williams D, Spradling AC. The expression profile of purified Drosophila germline stem cells. Dev Biol 2005, 283:486-502.
5. Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR. Conservation of core gene expression in vertebrate tissues. J Biol 2009, 8:33.
6. Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP. Gene expression during the life cycle of Drosophila melanogaster. Science 2002, 297:2270-2275.
7. 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.
8. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
9. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
10. Brem RB, Yvert G, Clinton R, Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science 2002, 296:752-755.
11. Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B. Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature 2007, 450:233-237.
12. Reimers M. Making informed choices about microarray data analysis. PLoS Computat Biol 2010, 6:e1000786.
13. Tan PK, Downey TJ, Spitznagel EL, 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. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Jedlicka AE, Kawasaki E, Martínez-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.
15. Fare TL, Coffey EM, Dai H, He YD, Kessler DA, Kilian KA, Koch JE, LeProust E, Marton MJ, Meyer MR, Stoughton RB, Tokiwa GY, Yang Y. Effects of atmospheric ozone on microarray data quality. Anal Chem 2003, 75:4672-4675.
16. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Scherf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24:1151-1161.
17. Fan X, Lobenhofer EK, Chen M, Shi W, Huang J, Luo J, Zhang J, Walker SJ, Chu TM, Li L, Deng Y, Cheng Y, Fang H, Shi L, Tong W. Consistency of predictive signature genes and classifiers generated using different microarray platforms. Pharmacogenomics J 2010, 10:247-257.
18. Luo J, Schumacher M, Scherer A, Sanoudou D, Megherbi D, Davison T, Shi T, Tong W, Shi L, Hong H, Zhao C, Elloumi F, Shi W, Thomas R, Lin S, Tillinghast G, Liu G, Zhou Y, Herman D, Li Y, Deng Y, Fang H, Bushel P, Woods M, Zhang J. A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data. Pharmacogenomics J 2010, 10:278-291.
19. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010, 28:827-838.
20. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, et al. The genome sequence of Drosophila melanogaster. Science 2000, 287:2185-2195.
21. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9:387-402.
22. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
23. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628.
24. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321:956-960.
25. Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, et al. Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 2009, 10:161.
26. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517.
27. Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ. A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics 2010, 11:282.
28. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133:523-536.
29. Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M. Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics 2010, 11:383.
30. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316:1484-1488.
31. Kapranov P, Willingham AT, Gingeras TR. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 2007, 8:413-423.
32. Klebanov L, Yakovlev A. How high is the level of technical noise in microarray data?. Biol Direct 2007, 2:9.
33. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515.
34. Richard H, Schulz MH, Sultan M, Nurnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M, Haas SA, Yaspo ML. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res 2010, 38:e112.
35. Telonis-Scott M, Kopp A, Wayne ML, Nuzhdin SV, McIntyre LM. Sex-specific splicing in Drosophila: widespread occurrence, tissue specificity and evolutionary conservation. Genetics 2009, 181:421-434.
36. Auer PL, Doerge RW. Statistical design and analysis of RNA sequencing data. Genetics 2010, 185:405-416.
37. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, et al. The developmental transcriptome of Drosophila melanogaster. Nature 2011, 471:473-479.
38. Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 2010, 38:e131.
39. Li J, Jiang H, Wong WH. Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol 2010, 11:R50.
40. Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010, 11:94.
41. Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11:R86.
42. Schatz MC. The missing graphical user interface for genomics. Genome Biol 2010, 11:128.
43. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH, . modENCODE Consortium Unlocking the secrets of the genome. Nature 2009, 459:927-930. modENCODE Consortium.
44. Nagalakshmi U, Waern K, Snyder M. RNA-Seq: a method for comprehensive transcriptome analysis. Curr Protoc Mol Biol 2010, 89:4.11.1-4.11.13.
45. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25.
46. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
47. Liu S, Lin L, Jiang P, Wang D, Xing Y. A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res 2010, 39:578-588.
48. Gnad F, Parsch J. Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression. Bioinformatics 2006, 22:2577-2579.
49. Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA. Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics 2009, 10:221.
50. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.
51. Malone JH, Oliver B. Sex-biased expression in heads of three Drosophila species and mRNA-Seq of head tissue from Drosophila pseudoobscura. Gene Expression Omnibus 2010, under entries GSE19989 and GSE23309., http://www.ncbi.nlm.nih.gov/geo/