BarleyBase--an expression profiling database for plant genomics - PubMed (original) (raw)

BarleyBase--an expression profiling database for plant genomics

Lishuang Shen et al. Nucleic Acids Res. 2005.

Abstract

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.

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Figures

Figure 1

Figure 1

Boxplots can be used to visualize overall experimental quality before expression data normalization. The central box shows the middle 50% of the data. The dotted lines or whiskers, extend to the 10th and 90th percentiles, respectively. The circles represent outliers. Boxes with the same color are technical replicates with the same treatment factors. These data summarize the logarithm of the raw probe set perfect match (PM) expression values in experiment BB4 before normalization.

Figure 2

Figure 2

Annotation for exemplar Barley1_11969. The exemplar annotation page includes the probe alignment, links to databases such as Gramene, PlantGDB and GrainGenes along with the best BLAST hits. The left-hand side picture shows the normalized expression data for some of the hybridizations in experiment BB4. The blocks at the bottom show the experimental factors laid out in a factorial experimental design. The raw probe intensity data PM (red) and MM (blue) levels for exemplar Barley1_11969 in hybridizations 17 and 18 in experiment BB4 show the different responses across the probe pairs.

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