Abstract
BackgroundLegumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose.DescriptionThe Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip® Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/.ConclusionsThe MtGEA web server has a well managed rich data set, and offers data retrieval and analysis tools provided in the web platform. It's proven to be a powerful resource for plant biologists to effectively and efficiently identify Medicago transcripts of interest from a multitude of aspects, formulate hypothesis about gene function, and overall interpret the Medicago genome from a systematic point of view.
Highlights
Legumes (Leguminosae or Fabaceae) play a major role in agriculture
To maximize the use of publicly-available Affymetrix GeneChip data and aid efforts to interpret the Medicago genome through functional genomics, we have developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server, available at http://bio info.noble.org/gene-atlas/
Transcription Factor Prediction The MtGEA server indexes 1,169 transcription factor (TF) genes belonging to 48 families, which were identified previously [38]. We identified another 129 putative novel TF genes from consensus sequences based on the presence of DNA binding domains in the predicted proteins
Summary
Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. The web server hosts gene expression data from 156 Affymetrix GeneChip® Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Legumes (Leguminosae or Fabaceae) play a major role in agriculture the world over, accounting for one-third of the world's crop production. Seeds from legumes such as common bean, soybean, chickpea, and lentil are staple foods in many parts of the world and are important sources of protein, lipid, carbohydrate, and minerals while forage legumes such as alfalfa and clover are important sources of nutrition for livestock [1]. Legume research is diverse and includes work on plant development, especially nodule and seed development, and plant responses to biotic and abiotic stresses
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