Development and evaluation of an Arabidopsis whole genome Affymetrix probe array - PubMed (original) (raw)
Development and evaluation of an Arabidopsis whole genome Affymetrix probe array
Julia C Redman et al. Plant J. 2004 May.
Free article
Abstract
We describe the development of a high-density Arabidopsis'whole genome' oligonucleotide probe array for expression analysis (the Affymetrix ATH1 GeneChip probe array) that contains approximately 22 750 probe sets. Precedence on the array was given to genes for which either expression evidence or a credible database match existed. The remaining space was filled with 'hypothetical' genes. The new ATH1 array represents approximately 23 750 genes of which 60% were detected in RNA from cultured seedlings. Sensitivity of the array, determined using spiking controls, was approximately one transcript per cell. The array demonstrated high technical reproducibility and concordance with real-time PCR results. Indole-3 acetic acid (IAA)-induced changes in gene expression were used for biological validation of the array. A total of 222 genes were significantly upregulated and 103 significantly downregulated by exposure to IAA. Of the genes whose products could be functionally classified, the largest specific classes of upregulated genes were transcriptional regulators and protein kinases, many fewer of which were represented among the downregulated genes. Over one-third of the auxin-regulated genes have no known function, although many belong to gene families with members that have previously been shown to be auxin regulated. For the 6714 genes represented both on this and the earlier Arabidopsis Genome (AG) array, both signal intensities and gene expression ratios were very similar. Mapping of the oligonucleotides on the ATH1 array to the latest (version 4.0) annotation showed that over 95% of the probe sets (based on version 2.0 annotation) still fully represented their original target genes.
Similar articles
- Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice.
Jain M, Khurana JP. Jain M, et al. FEBS J. 2009 Jun;276(11):3148-62. doi: 10.1111/j.1742-4658.2009.07033.x. Epub 2009 Apr 28. FEBS J. 2009. PMID: 19490115 - The HAT2 gene, a member of the HD-Zip gene family, isolated as an auxin inducible gene by DNA microarray screening, affects auxin response in Arabidopsis.
Sawa S, Ohgishi M, Goda H, Higuchi K, Shimada Y, Yoshida S, Koshiba T. Sawa S, et al. Plant J. 2002 Dec;32(6):1011-22. doi: 10.1046/j.1365-313x.2002.01488.x. Plant J. 2002. PMID: 12492842 - Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis.
Goda H, Sawa S, Asami T, Fujioka S, Shimada Y, Yoshida S. Goda H, et al. Plant Physiol. 2004 Apr;134(4):1555-73. doi: 10.1104/pp.103.034736. Epub 2004 Mar 26. Plant Physiol. 2004. PMID: 15047898 Free PMC article. - An Arabidopsis basic helix-loop-helix leucine zipper protein modulates metal homeostasis and auxin conjugate responsiveness.
Rampey RA, Woodward AW, Hobbs BN, Tierney MP, Lahner B, Salt DE, Bartel B. Rampey RA, et al. Genetics. 2006 Dec;174(4):1841-57. doi: 10.1534/genetics.106.061044. Epub 2006 Oct 8. Genetics. 2006. PMID: 17028341 Free PMC article. - Genetics of Aux/IAA and ARF action in plant growth and development.
Liscum E, Reed JW. Liscum E, et al. Plant Mol Biol. 2002 Jun-Jul;49(3-4):387-400. Plant Mol Biol. 2002. PMID: 12036262 Review.
Cited by
- The Adaxial/Abaxial Patterning of Auxin and Auxin Gene in Leaf Veins Functions in Leafy Head Formation of Chinese Cabbage.
Yue X, Su T, Xin X, Li P, Wang W, Yu Y, Zhang D, Zhao X, Wang J, Sun L, Jin G, Yu S, Zhang F. Yue X, et al. Front Plant Sci. 2022 Jun 9;13:918112. doi: 10.3389/fpls.2022.918112. eCollection 2022. Front Plant Sci. 2022. PMID: 35755702 Free PMC article. - IQD1 Involvement in Hormonal Signaling and General Defense Responses Against Botrytis cinerea.
Barda O, Levy M. Barda O, et al. Front Plant Sci. 2022 Apr 26;13:845140. doi: 10.3389/fpls.2022.845140. eCollection 2022. Front Plant Sci. 2022. PMID: 35557724 Free PMC article. - Lectin receptor-like kinase LecRK-VIII.2 is a missing link in MAPK signaling-mediated yield control.
Xiao W, Hu S, Zou X, Cai R, Liao R, Lin X, Yao R, Guo X. Xiao W, et al. Plant Physiol. 2021 Sep 4;187(1):303-320. doi: 10.1093/plphys/kiab241. Plant Physiol. 2021. PMID: 34618128 Free PMC article. - Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.
Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Ambrosino L, et al. Plants (Basel). 2020 May 6;9(5):591. doi: 10.3390/plants9050591. Plants (Basel). 2020. PMID: 32384671 Free PMC article. Review. - An integrated analysis of cell-type specific gene expression reveals genes regulated by REVOLUTA and KANADI1 in the Arabidopsis shoot apical meristem.
Ram H, Sahadevan S, Gale N, Caggiano MP, Yu X, Ohno C, Heisler MG. Ram H, et al. PLoS Genet. 2020 Apr 15;16(4):e1008661. doi: 10.1371/journal.pgen.1008661. eCollection 2020 Apr. PLoS Genet. 2020. PMID: 32294082 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases