Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise and Julie A. Dickerson

Please cite BarleyBase using this paper if your publication use tools and data from BarleyBase.

 BarleyBase (BB) (www.barleybase.org) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. BB houses raw and normalized expression data from the two publicly available Affymetrix genome arrays, Barley1 and Arabidopsis ATH1 with plans to include the new Affymetrix 61K wheat, maize, soybean and rice arrays, as they become available. BB contains a broad set of query and display options at all data levels, ranging from experiments to individual hybridizations to probe sets down to individual probes. Users can perform cross-experiment queries on probe sets based on observed expression profiles and/or based on known biological information. Probe set queries are integrated with visualization and analysis tools such as the R statistical toolbox, data filters and a large variety of plot types. Controlled vocabularies for gene and plant ontologies, as well as interconnecting links to physical or genetic map and other genomic data in PlantGDB, Gramene and GrainGenes, allow users to perform EST alignments and gene function prediction using Barley1 exemplar sequences, thus, enhancing cross-species comparison.

Ibrahim AF, Hedley PE, Cardle L, Kruger W, Marshall DF, Muehlbauer GJ, Waugh R.

 A number of methods are currently used for gene expression profiling. They differ in scale, economy and sensitivity. We present the results of a direct comparison between serial analysis of gene expression (SAGE) and the Barley1 Affymetrix GeneChip. Both technology platforms were used to obtain quantitative measurements of transcript abundance using identical RNA samples and assessed for their ability to quantify differential gene expression. For SAGE, a total of 82,122 tags were generated from two independent libraries representing whole developing barley caryopsis and dissected embryos. The Barley1 GeneChip contains 22,791 probe sets. Results obtained from both methods are generally comparable, indicating that both will lead to similar conclusions regarding transcript levels and differential gene expression. However, excluding singletons, 24.4% of the unique SAGE tags had no corresponding probe set on the Barley1 array indicating that a broader snapshot of gene expression was obtained by SAGE. Discrepancies were observed for a number of "genes" and these are discussed.

Xinping Cui, Jin Xu, Rehana Asghar, Pascal Condamine, Jan T. Svensson, Steve Wanamaker, Nils Stein, Mikeal Roose, and Timothy J. Close

 Motivation: Borevitz et al. (2003) hybridized genomic DNA to oligonucleotide microarrays to identify single-feature polymorphisms (SFP) for Arabidopsis, which has a genome size of about 130 megabase pairs (Mbp). However, that method does not work well for organisms such as barley, with a much larger 5,200 Mbp genome. Here we demonstrate SFP detection using a small number of replicate datasets and complex RNA as a surrogate for barley DNA. To identify single probes defining SFPs in the data, we developed a method using robustified projection pursuit (RPP). This method first evaluates, for each probe set, the overall differentiation of signal intensities between two genotypes and then measures the contribution of the individual probes within the probe set to the overall differentiation.

Results: RNA from whole seedlings with and without dehydration stress provided "present" calls for about 75% of probe sets. Using triplicated data, among the 5% of "present" probe sets identified as most likely to contain at least one SFP probe at least 80% are correctly predicted. This was determined by direct sequencing of PCR amplicons derived from barley genomic DNA. Using a 5 percentile cutoff, we defined 2007 SFP probes contained in 1684 probe sets by combining three parental genotype comparisons: Steptoe vs. Morex, Morex vs. Barke and Oregon Wolfe Barley Dominant vs. Recessive (see supplemental tables).

Availability: The algorithm is available upon request from the corresponding author.

Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J, Cardle L, Marshall DF, Waugh R.

ABSTRACT : A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.

PMID: 15960806 [PubMed - in process]

Tang X, Shen L, Dickerson JA.

 SUMMARY: BarleyExpress is a web-based microarray experiment data submission tool for BarleyBase, a public data resource of Affymetrix GeneChip(R) data for cereals. BarleyExpress uses the Plant Ontology vocabularies and enhances the MIAME guidelines to standardize the annotation of microarray gene expression experiments. BarleyExpress also provides explicit support for factorial experiment design and template loading methods to ease the submission process for large experiments. AVAILABILITY: http://barleybase.org. SUPPLEMENTARY INFORMATION: BarleyExpress Users Manual.
PMID: 15347571 [PubMed - as supplied by publisher]

Rico A. Caldo, Dan Nettleton and Roger P. Wise

Nancy A. Eckardt, News and Reviews Editor

Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, Oldroyd GE, Long SR.

Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP.