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. 2004 Apr;5(3):245–252. doi: 10.1002/cfg.397

A Comparison of Global Gene Expression Measurement Technologies in Arabidopsis thaliana

Sean J Coughlan 1,✉, Vikas Agrawal 2, Blake Meyers 2
PMCID: PMC2447440  PMID: 18629150

Abstract

Microarrays and tag-based transcriptional profiling technologies represent diverse but complementary data types. We are currently conducting a comparison of high-density in situ synthesized microarrays and massively-parallel signature sequencing (MPSS) data in the model plant, Arabidopsis thaliana. The MPSS data (available at http://mpss.udel.edu/at) and the microarray data have been compiled using the same RNA source material. In this review, we outline the experimental strategy that we are using, and present preliminary data and interpretations from the transcriptional profiles of Arabidopsis leaves and roots. The preliminary data indicate that the log ratio differences of transcripts between leaves and roots measured by microarray data are in better agreement with the MPSS data than the absolute intensities measured for individual microarrays hybridized to only one of the cRNA populations. The correlation was substantially improved by focusing on a subset of genes excluding those with very low expression levels; this selection may have removed noisy data. Future reports will incorporate more than 10 tissues that have been sampled by MPSS.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14;408(6814):796–815. doi: 10.1038/35048692. [DOI] [PubMed] [Google Scholar]
  2. Brenner S., Johnson M., Bridgham J., Golda G., Lloyd D. H., Johnson D., Luo S., McCurdy S., Foy M., Ewan M. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol. 2000 Jun;18(6):630–634. doi: 10.1038/76469. [DOI] [PubMed] [Google Scholar]
  3. Goff Stephen A., Ricke Darrell, Lan Tien-Hung, Presting Gernot, Wang Ronglin, Dunn Molly, Glazebrook Jane, Sessions Allen, Oeller Paul, Varma Hemant. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science. 2002 Apr 5;296(5565):92–100. doi: 10.1126/science.1068275. [DOI] [PubMed] [Google Scholar]
  4. Hughes T. R., Mao M., Jones A. R., Burchard J., Marton M. J., Shannon K. W., Lefkowitz S. M., Ziman M., Schelter J. M., Meyer M. R. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol. 2001 Apr;19(4):342–347. doi: 10.1038/86730. [DOI] [PubMed] [Google Scholar]
  5. Iacobuzio-Donahue Christine A., Ashfaq Raheela, Maitra Anirban, Adsay N. Volkan, Shen-Ong Grace L., Berg Karin, Hollingsworth Michael A., Cameron John L., Yeo Charles J., Kern Scott E. Highly expressed genes in pancreatic ductal adenocarcinomas: a comprehensive characterization and comparison of the transcription profiles obtained from three major technologies. Cancer Res. 2003 Dec 15;63(24):8614–8622. [PubMed] [Google Scholar]
  6. Ishii M., Hashimoto S., Tsutsumi S., Wada Y., Matsushima K., Kodama T., Aburatani H. Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis. Genomics. 2000 Sep 1;68(2):136–143. doi: 10.1006/geno.2000.6284. [DOI] [PubMed] [Google Scholar]
  7. Jin W., Riley R. M., Wolfinger R. D., White K. P., Passador-Gurgel G., Gibson G. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet. 2001 Dec;29(4):389–395. doi: 10.1038/ng766. [DOI] [PubMed] [Google Scholar]
  8. Kuo Winston Patrick, Jenssen Tor-Kristian, Butte Atul J., Ohno-Machado Lucila, Kohane Isaac S. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. 2002 Mar;18(3):405–412. doi: 10.1093/bioinformatics/18.3.405. [DOI] [PubMed] [Google Scholar]
  9. Lee M. L., Kuo F. C., Whitmore G. A., Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):9834–9839. doi: 10.1073/pnas.97.18.9834. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Lockhart D. J., Dong H., Byrne M. C., Follettie M. T., Gallo M. V., Chee M. S., Mittmann M., Wang C., Kobayashi M., Horton H. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996 Dec;14(13):1675–1680. doi: 10.1038/nbt1296-1675. [DOI] [PubMed] [Google Scholar]
  11. Shoemaker D. D., Schadt E. E., Armour C. D., He Y. D., Garrett-Engele P., McDonagh P. D., Loerch P. M., Leonardson A., Lum P. Y., Cavet G. Experimental annotation of the human genome using microarray technology. Nature. 2001 Feb 15;409(6822):922–927. doi: 10.1038/35057141. [DOI] [PubMed] [Google Scholar]
  12. Tan Paul K., Downey Thomas J., Spitznagel Edward L., Jr, Xu Pin, Fu Dadin, Dimitrov Dimiter S., Lempicki Richard A., Raaka Bruce M., Cam Margaret C. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 2003 Oct 1;31(19):5676–5684. doi: 10.1093/nar/gkg763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Velculescu V. E., Zhang L., Vogelstein B., Kinzler K. W. Serial analysis of gene expression. Science. 1995 Oct 20;270(5235):484–487. doi: 10.1126/science.270.5235.484. [DOI] [PubMed] [Google Scholar]
  14. Wisman E., Ohlrogge J. Arabidopsis microarray service facilities. Plant Physiol. 2000 Dec;124(4):1468–1471. doi: 10.1104/pp.124.4.1468. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Wortman Jennifer R., Haas Brian J., Hannick Linda I., Smith Roger K., Jr, Maiti Rama, Ronning Catherine M., Chan Agnes P., Yu Chunhui, Ayele Mulu, Whitelaw Catherine A. Annotation of the Arabidopsis genome. Plant Physiol. 2003 Jun;132(2):461–468. doi: 10.1104/pp.103.022251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Yu Jun, Hu Songnian, Wang Jun, Wong Gane Ka-Shu, Li Songgang, Liu Bin, Deng Yajun, Dai Li, Zhou Yan, Zhang Xiuqing. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 2002 Apr 5;296(5565):79–92. doi: 10.1126/science.1068037. [DOI] [PubMed] [Google Scholar]
  17. Zhu T., Wang X. Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol. 2000 Dec;124(4):1472–1476. doi: 10.1104/pp.124.4.1472. [DOI] [PMC free article] [PubMed] [Google Scholar]

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