Abstract
BackgroundExperiments using whole transcriptome microarrays produce massive amounts of data. To gain a comprehensive understanding of this gene expression data it needs to be integrated with other available information such as gene function and metabolic pathways. Bioinformatics tools are essential to handle, organize and interpret the results. To date, no database provides whole transcriptome analysis capabilities integrated with terms describing biological functions for soybean (Glycine max (L) Merr.). To this end we have developed SoyXpress, a relational database with a suite of web interfaces to allow users to easily retrieve data and results of the microarray experiment with cross-referenced annotations of expressed sequence tags (EST) and hyperlinks to external public databases. This environment makes it possible to explore differences in gene expression, if any, between for instance transgenic and non-transgenic soybean cultivars and to interpret the results based on gene functional annotations to determine any changes that could potentially alter biological processes.ResultsSoyXpress is a database designed for exploring the soybean transcriptome. Currently SoyXpress houses 380,095 soybean Expressed Sequence Tags (EST), linked with metabolic pathways, Gene Ontology terms, SwissProt identifiers and Affymetrix gene expression data. Array data is presently available from an experiment profiling global gene expression of three conventional and two genetically engineered soybean cultivars. The microarray data is linked with the sequence data, for maximum knowledge extraction. SoyXpress is implemented in MySQL and uses a Perl CGI interface.ConclusionSoyXpress is designed for the purpose of exploring potential transcriptome differences in different plant genotypes, including genetically modified crops. Soybean EST sequences, microarray and pathway data as well as searchable and browsable gene ontology are integrated and presented. SoyXpress is publicly accessible at .
Highlights
Experiments using whole transcriptome microarrays produce massive amounts of data
We present SoyXpress, where we have integrated 380,095 soybean expressed sequence tags (EST) sequences and Affymetrix microarray data with functional annotations such as metabolic pathways and gene ontology
After receiving the query ID, the corresponding EST sequence, Affymetrix probe sequence and DFCI/TIGR TC contig will be retrieved from our database
Summary
Experiments using whole transcriptome microarrays produce massive amounts of data. To gain a comprehensive understanding of this gene expression data it needs to be integrated with other available information such as gene function and metabolic pathways. No database provides whole transcriptome analysis capabilities integrated with terms describing biological functions for soybean (Glycine max (L) Merr.) To this end we have developed SoyXpress, a relational database with a suite of web interfaces to allow users to retrieve data and results of the microarray experiment with cross-referenced annotations of expressed sequence tags (EST) and hyperlinks to external public databases. This environment makes it possible to explore differences in gene expression, if any, between for instance transgenic and non-transgenic soybean cultivars and to interpret the results based on gene functional annotations to determine any changes that could potentially alter biological processes. Many other communities develop resource databases, building the tools and functions to suit their organism, for example BarleyBase/PlexDB [3] for Barley genomics, MELOGEN [4] for melon genomics and the Tomato Expression Database (TED) [5]
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