ArticleBMC genomics2008
SoyXpress: a database for exploring the soybean transcriptome.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Decoding the landscape of cell-type-specific co-expressed transcription factors in soybean.Nature plants · 2026Article
- Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes.Molecular genetics and genomics : MGG · 2018Article
- ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism.BMC plant biology · 2015Article
- Expanding Omics Resources for Improvement of Soybean Seed Composition Traits.Frontiers in plant science · 2015Review
- SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways.BMC genomics · 2014Article
- SoyFN: a knowledge database of soybean functional networks.Database : the journal of biological databases and curation · 2014Article
- Managing major data of genetically modified mice: from scientific demands to legal obligations.Transgenic research · 2012Article
- Cell wall, lignin and fatty acid-related transcriptome in soybean: Achieving gene expression patterns for bioenergy legume.Genetics and molecular biology · 2012Article
- A web-based bioinformatics interface applied to the GENOSOJA Project: Databases and pipelines.Genetics and molecular biology · 2012Article
- Expectations, validity, and reality in gene expression profiling.Journal of clinical epidemiology · 2010Review
- A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences.Annals of botany · 2010Article
- SoyDB: a knowledge database of soybean transcription factors.BMC plant biology · 2010Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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 http://soyxpress.agrenv.mcgill.ca.
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Registered trials
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