1. Lipschutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ: High density
synthetic oligonucleotide arrays. Nature Genetics 1999,
21:20-24.
2. Henning L, Menges M, Murray JA, Gruissem W: Arabidopsis transcript
profiling on Affymetrix GeneChip arrays. Plant Molecular
Biology 2003, 53:457-465.
3. Zhu T, Wang X: Large scale profiling of the Arabidopsis transcriptome.
Plant Physiology 2000, 124:1472-1476.
4. Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S: NASCArrays:
A repository for microarray data generated by NASC's
transcriptomics service. Nucleic Acids Research 2004,
32:D575-D577.
5. Redman RD, Schwartz C, Morel JL, Edmondson J: Development
and evaluation of an Arabidopsis whole genome Affymetrix
probe array. Plant Journal 2004, 38:545-561.
6. Grigoryev DM, Ma S-F, Simon BA, Irizarrt RA, Ye SQ, Garcia JGN: In
vitro identification and in silico utilization of interspecies
sequence similarities using GeneChip® technology. BMC
Genomics 2005, 6:62.
7. Seo J, Hoffman EP: Probe-set algorithms: Is there a rational
best bet? BMC Bioinformatics 2006, 7:395.
8. Affymetrix Microarray Suite User Guide [http://www.affyme
trix.com/support/technical/manuals.affx]
9. Li C, Wong WH: Model-based analysis of oligonucleotide
arrays: expression index computation and outlier detection.
Proceedings of the National Academy of Sciences of the United States of
America 2001, 98:31-36.
10. Li C, Wong WH: Model-based analysis of oligonucleotide
arrays: design issues and standard error application. Genome
Biology 2001, 2:0032.1-0032.11.
11. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ,
Scherf U, Speed TB: Exploration, normalization, and summaries
of high density oligonucleotide array probe level data.
Biostatistics 2003, 4:249-264.
12. Zhang L, Miles MF, Aldape KD: A model of molecular interactions
on short oligonucleotide microarrays. Nature Biotechnology
2003, 21:818-821.
13. Wu Z, Irizarry RA: Reprocessing of oligonucleotide array data.
Nature Biotechnology 2004, 22:656-658.
14. Chismar JD, Mondala T, Fox HS, Roberts E, Langford D, Masliah E,
Salomon DR, Head SR: Analysis of results variability from highdensity
oligonucleotide arrays comparing same-species and
cross-species hybridisations. Biotechniques 2002, 33:516-524.
15. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, Giavalisco P,
Nieslt-Struwe K, Muchmore E, Varki A, Ravid R, Doxiadis GM, Bontrop
RE, Paabo S: Intra- and interspecific variation in primate
gene expression patterns. Science 2002, 296:340-343.
16. Caceres M, Lachuer J, Zapala MA, Redmond JC, Kudo L, Geschwind
DH, Lockhart DJ, Preuss TM, Barlow C: Elevated gene expression
levels distinguish human from non-human primate brains.
Proceedings of the National Academy of Sciences of the United States of
America 2003, 100:13030-13035.
17. Higgins MA, Berridge BR, Mills BJ, Schultze AE, Gao H, Searfoss GH,
Baker TK, Ryan TP: Gene expression analysis of the acute
phase response using a canine microarray. Toxicological Sciences
2003, 74:470-484.
18. Becher M, Talke IN, Krall L, Krämer U: Cross-species microarray
transcript profiling reveals high constitutive expression of
metal homeostasis genes in shoots of the zinc hyperaccumulator
Arabidopsis halleri. Plant Journal 2004, 37:251-268.
19. Khaitovich P, Weiss G, Lachmann M, Hellman I, Enard W, Muetzel B,
Wirkner U, Ansorge W, Paabo S: A neutral model of transcriptome
evolution. Public Library of Science Biology 2004, 2:682-689.
20. Uddin M, Wildman DE, Liu GZ, Xu WB, Johnson RM, Hof PR, Kapatos
G, Grossman LI, Goodman M: Sister grouping of chimpanzees
and humans as revealed by genome-wide phylogenetic
analysis of brain gene expression profiles. Proceedings of the
National Academy of Sciences of the United States of America 2004,
101:2957-2962.
21. Weber M, Harada E, Vess C, van Roepenack-Lahaye E, Clemens S:
Comparitive microarray analysis of Arabidopsis thaliana and
Arabidopsis halleri roots identifies nicotinamine synthase, a
ZIP transporter and other genes as potential metal hyperaccumulation
factors. Plant Journal 2004, 37:269-281.
22. Hammond JP, Broadley MR, Craigon DJ, Higgins J, Emmerson ZF,
Townsend HJ, White PJ, May ST: Using genomic DNA-based
probe-selection to improve the sensitivity of high-density oligonucleotide
arrays when applied to heterologous species.
Plant Methods 2005, 1:10.
23. Hammond JP, Bowen HC, White PJ, Mills V, Pyke KA, Baker AJM,
Whiting SN, May ST, Broadley MR: A comparison of the Thlaspi
caerulescens and Thlaspi arvense shoot transcriptomes. New
Phytologist 2006, 170:239-260.
24. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M,
Schölkopf B, Weigel D, Lohmann J: A gene expression map of
Arabidopsis development. Nature Genetics 2005, 37:501-506.
25. PlexDb database [http://www.plexdb.org]
26. Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker
SI, Mandal J, Xu J, Cui X, Close TJ: Comparative transcriptional
profiling of two contrasting rice genotypes under
salinity stress during vegetative growth stage. Plant Physiology
2005, 139:822-835.
27. Mei R, Hubbell E, Bekiranov S, Mittmann M, Christians FC, Shen MM,
Lu G, Fang J, Liu WM, Ryder T, Kaplan P, Kulp D, Webster TA:
Probe selection for high-density oligonucleotide arrays. Proceedings
of the National Academy of Sciences of the United States of America
2003, 100:11237-11242.
28. Ji W, Zhou WL, Gregg K, Yu N, Davis S, Davis S: A method for
cross-species gene expression analysis with high-density oligonucleotide
arrays. Nucleic Acids Research 2004, 32:e93.
29. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W-R:
Genome-wide identification of superior reference genes for
transcript normalisation in Arabidopsis. Plant Physiology 2005,
139:5-17.
30. Shen L, Gong J, Caldo RA, Nettleton D, Cook D, Wise RP, Dickerson
JA: BarleyBase – An expression profiling database for plant
genomics. Nucleic Acids Research 2005, 33:D614-D618.
31. Xspecies .cel file parser Version 1.1.and Version 2 [http://
affymetrix.arabidopsis.info/xspecies/]
32. Affymetrix [http://www.affymetrix.com]
33. NASCarrays [http://affymetrix.arabidopsis.info]