Benchmarking the CATMA microarray. A novel tool for arabidopsis transcriptome analysis

Plant Physiology

Volumn 137, Issue 2, 2005, Pages 588-601

  Allemeersch, Joke ^a   Durinck, Steffen ^a   Vanderhaeghen, Rudy ^b   Alard, Philippe ^b   Maes, Ruth ^b   Seeuws, Kurt ^b   Bogaert, Tom ^b   Coddens, Kathleen ^b   Deschouwer, Kirsten ^b   Van Hummelen, Paul ^b   Vuylsteke, Marnik ^b   Moreau, Yves ^a   Kwekkeboom, Jeroen ^c   Wijfjes, André H M ^c   May, Sean ^d   Beynon, Jim ^e   Hilson, Pierre ^b   Kuiper, Martin T R ^b  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c ServiceXS   (Netherlands)

^d UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^e UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE; GENES; RNA; SENSITIVITY ANALYSIS;

CATMA MICROARRAYS; OLIGONUCLEOTIDES; RNA SAMPLES;

PLANTS (BOTANY);

GENES; NUCLEIC ACIDS; PLANTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

MESSENGER RNA; PLANT RNA;

ARABIDOPSIS; ARTICLE; COMPARATIVE STUDY; DNA MICROARRAY; GENE EXPRESSION; GENETICS; LABORATORY DIAGNOSIS; METHODOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

ARABIDOPSIS; FALSE NEGATIVE REACTIONS; FALSE POSITIVE REACTIONS; GENE EXPRESSION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; RNA, PLANT; SENSITIVITY AND SPECIFICITY;

EID: 21044441648     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.051300     Document Type: Article

References (34)

1. Affymetrix (2001) Microarray Suite User Guide, Version 5. http://www. affymetrix.com/products/software/specific/mas.affx. (November, 2004)
2. Agilent (2003) Feature Extraction Software User Manual, Version 7.1. http://www.chem.agilent.com/Scripts/PDS.asp?1Page=2547. (February, 2004)
3. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
4. Barczak A, Rodriguez WM, Hanspers K, Koth LL, Chuan Tai Y, Bolstad BM, Speed TP, Erle DJ (2003) Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res 13: 1775-1785
5. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 57: 289-300
6. Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, Mueller LA, Yoon J, Doyle A, Lander G, et al (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol 135: 745-755
7. Boyes DC, Zayed AM, Ascenzi R, McCaskill AJ, Hoffman NE, Davis KR, Gorlach J (2001) Growth stage-based phenotypic analysis of Arabidopsis: a model for high throughput functional genomics in plants. Plant Cell 13: 1499-1510
8. Chudin E, Walker R, Kosaka A, Wu SX, Rabert D, Chang TK, Kreder DE (2002) Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays. Genome Biol 3: RESEARCH0005
9. Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S (2004) NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res 32: D575-D577
10. Crowe ML, Serizet C, Thareau V, Aubourg S, Rouzé P, Hilson P, Beynon J, Weisbeek P, Van Hummelen P, Reymond P, et al (2003) CATMA: a complete Arabidopsis GST database. Nucleic Acids Res 31: 156-158
11. D'Haeseleer P, Liang S, Somogyi R (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16: 707-726
12. Ferl GZ, Timmerman JM, Witte ON (2003) Extending the utility of gene profiling data by bridging microarray platforms. Proc Natl Acad Sci USA 100: 10585-10587
13. Gentleman RC, Carey VJ, Bates DJ, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.1-R80.16
14. Hilson P, Allemeersch J, Altmann T, Aubourg S, Avon A, Beynon J, Bhalerao RP, Bitton F, Caboche M, Cannoot B, et al (2004) Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res 14: 2176-2189
15. Hilson P, Small I, Kuiper MTR (2003) European consortia building integrated resources for Arabidopsis functional genomics. Curr Opin Plant Biol 6: 426-429
16. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, et al (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126
17. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264
18. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18: 405-412
19. Lee JK, Bussey KJ, Gwadry FG, Reinhold W, Riddick G, Pelletier SL, Nishizuka S, Szakacs G, Annereau JP, Shankavaram U, et al (2003) Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biol 4: R82.1-R82.12
20. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, et al (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804
21. Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyere C, Caboche M, Debast C, Gualberto J, Hoffmann B, et al (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 16: 2089-2103
22. Maki Y, Tominaga D, Okamoto M, Watanabe S, Eguchi Y (2001) Development of a system for the inference of large scale genetic networks. Pac Symp Biocomput 2001: 446-458
23. Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M (2003) Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet 19: 570-577
24. Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS (2003) Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics 4: 27.1-27.12
25. Puskás LG, Zvara A, Hackler L Jr, Van Hummelen P (2002) RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 32: 1330-1340
26. Quackenbush J (2003) Genomics. Microarrays - guilt by association. Science 302: 240-241
27. Redman JC, Haas BJ, Tanimoto G, Town CD (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J 38: 545-561
28. Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM (2002) Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 62: 4427-4433
29. Schiex T, Moisan A, Rouzé P (2001) EUGÈNE: an eukaryoric gene finder that combines several sources of evidence. Lect Notes Comput Sci 2066: 111-125
30. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol 3, No 1, Article 3. http://www.bepress.com/ sagmb/vol3/iss1/art3. (January, 2005)
31. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440-9445
32. Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31: 5676-5684
33. Thareau V, Déhais P, Serizet C, Hilson P, Rouzé P, Aubourg S (2003) Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics 19: 2191-2198
34. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC (2002) Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res 30: e48