17181774

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0370003, umls-concept:C1513400, umls-concept:C1709016, umls-concept:C2347026, umls-concept:C2603343
pubmed:issue	3
pubmed:dateCreated	2007-1-24
pubmed:databankReference	http://linkedlifedata.com/resource/pubmed/xref/GENBANK/DQ480366, http://linkedlifedata.com/resource/pubmed/xref/GENBANK/DQ480367, http://linkedlifedata.com/resource/pubmed/xref/GENBANK/DQ480368, http://linkedlifedata.com/resource/pubmed/xref/GENBANK/DQ480369, http://linkedlifedata.com/resource/pubmed/xref/GEO/GPL3638, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSE4429, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSE4632, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSE5308, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM103772, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM103773, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM103774, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM103775, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM124754, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM124755, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM124756, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM124757, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM124758, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM124759, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM124760, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM124761, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM99793, http://linkedlifedata.com/resource/pubmed/xref/GEO/GSM99794
pubmed:abstractText	Studies of the behavior of biological systems often require monitoring of the expression of many genes in a large number of samples. While whole-genome arrays provide high-quality gene-expression profiles, their high cost generally limits the number of samples that can be studied. Although inexpensive small-scale arrays representing genes of interest could be used for many applications, it is challenging to obtain accurate measurements with conventional small-scale microarrays. We have developed a small-scale microarray system that yields highly accurate and reproducible expression measurements. This was achieved by implementing a stable gene-based quantile normalization method for array-to-array normalization, and a probe-printing design that allows use of a statistical model to correct for effects of print tips and uneven hybridization. The array measures expression values in a single sample, rather than ratios between two samples. This allows accurate comparisons among many samples. The array typically yielded correlation coefficients higher than 0.99 between technically duplicated samples. Accuracy was demonstrated by a correlation coefficient of 0.88 between expression ratios determined from this array and an Affymetrix GeneChip, by quantitative RT-PCR, and by spiking known amounts of specific RNAs into the RNA samples used for profiling. The array was used to compare the responses of wild-type, rps2 and ndr1 mutant plants to infection by a Pseudomonas syringae strain expressing avrRpt2. The results suggest that ndr1 affects a defense-signaling pathway(s) in addition to the RPS2-dependent pathway, and indicate that the microarray is a powerful tool for systems analyses of the Arabidopsis disease-signaling network.
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/9207397
pubmed:citationSubset	IM
pubmed:chemical	http://linkedlifedata.com/resource/pubmed/chemical/Arabidopsis Proteins, http://linkedlifedata.com/resource/pubmed/chemical/NDR1 protein, Arabidopsis, http://linkedlifedata.com/resource/pubmed/chemical/RPS2 protein, Arabidopsis, http://linkedlifedata.com/resource/pubmed/chemical/Transcription Factors
pubmed:status	MEDLINE
pubmed:month	Feb
pubmed:issn	0960-7412
pubmed:author	pubmed-author:CollerJohnJ, pubmed-author:DenouxCarineC, pubmed-author:DewdneyJuliaJ, pubmed-author:GlazebrookJaneJ, pubmed-author:KatagiriFumiakiF, pubmed-author:MitraRaka MRM, pubmed-author:SatoMasanaoM, pubmed-author:SpiveyNatalie WNW, pubmed-author:WangDongD
pubmed:issnType	Print
pubmed:volume	49
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	565-77
pubmed:meshHeading	pubmed-meshheading:17181774-Arabidopsis, pubmed-meshheading:17181774-Arabidopsis Proteins, pubmed-meshheading:17181774-Gene Expression Profiling, pubmed-meshheading:17181774-Models, Theoretical, pubmed-meshheading:17181774-Molecular Sequence Data, pubmed-meshheading:17181774-Nucleic Acid Amplification Techniques, pubmed-meshheading:17181774-Oligonucleotide Array Sequence Analysis, pubmed-meshheading:17181774-Plant Diseases, pubmed-meshheading:17181774-Reproducibility of Results, pubmed-meshheading:17181774-Signal Transduction, pubmed-meshheading:17181774-Transcription Factors
pubmed:year	2007
pubmed:articleTitle	A high-performance, small-scale microarray for expression profiling of many samples in Arabidopsis-pathogen studies.
pubmed:affiliation	Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Avenue, St Paul, MN 55108, USA.
pubmed:publicationType	Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Research Support, N.I.H., Extramural, Validation Studies