Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics
Open Access
- 21 October 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 39 (Database), D1156-D1163
- https://doi.org/10.1093/nar/gkq991
Abstract
Tomato Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. The database is functionally expanded from the previously described Tomato Expression Database by including metabolite profiles as well as large-scale tomato small RNA (sRNA) data sets. Computational pipelines have been developed to process microarray, metabolite and sRNA data sets archived in the database, respectively, and TFGD provides downloads of all the analyzed results. TFGD is also designed to enable users to easily retrieve biologically important information through a set of efficient query interfaces and analysis tools, including improved array probe annotations as well as tools to identify co-expressed genes, significantly affected biological processes and biochemical pathways from gene expression data sets and miRNA targets, and to integrate transcript and metabolite profiles, and sRNA and mRNA sequences. The suite of tools and interfaces in TFGD allow intelligent data mining of recently released and continually expanding large-scale tomato functional genomics data sets. TFGD is available at http://ted.bti.cornell.edu.Keywords
This publication has 29 references indexed in Scilit:
- Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomicsBMC Genomics, 2010
- Plant MetGenMAP: An Integrative Analysis System for Plant Systems BiologyPlant Physiology, 2009
- ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expressionNucleic Acids Research, 2009
- NCBI GEO: archive for high-throughput functional genomic dataNucleic Acids Research, 2009
- Flavour compounds in tomato fruits: identification of loci and potential pathways affecting volatile compositionJournal of Experimental Botany, 2008
- Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripeningGenome Research, 2008
- miRBase: tools for microRNA genomicsNucleic Acids Research, 2007
- A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thalianaGenes & Development, 2006
- Integrated Analysis of Metabolite and Transcript Levels Reveals the Metabolic Shifts That Underlie Tomato Fruit Development and Highlight Regulatory Aspects of Metabolic Network BehaviorPlant Physiology, 2006
- Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray ExperimentsStatistical Applications in Genetics and Molecular Biology, 2004