Table I. Databases, data mining, and analysis tools for root systems biology.
Freely available databases and mining tools for root systems biology are listed. Many of these databases also may be useful for the study of other plant organs and systems.
| Resource | Description | Reference |
|---|---|---|
| VirtualPlant 1.3 (http://www.virtualplant.org) | Integrates genomic data and provides visualization and analysis tools to aid the generation of biological hypotheses; also includes predicted and validated protein-DNA interactions | Katari et al. (2010) |
| Sungear (http://virtualplant.bio.nyu.edu/cgi-bin/sungear/index.cgi) | Enables rapid, visually interactive exploration of large sets of genomic data; allows browsing of gene sets by experiment, gene annotation, and ontological term; makes otherwise complicated queries quick and visually intuitive | Part of the VirtualPlant suite of tools |
| Arabidopsis eFP Browser (http://bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi) | Enables the visualization of relative and absolute gene expression data from approximately 22,000 Arabidopsis genes in different tissues and under a variety of conditions | Winter et al. (2007) |
| GENIUS (Gene Network Inference Using Signatures; http://networks.bio.puc.cl/genius/) | Uses large-scale gene expression data to identify signatures that characterize and discriminate the process of interest, and then uses these signatures to predict a functional gene network | |
| VisuaLRTC | Lateral root transcriptome compendium | Parizot et al. (2010) |
| iRootHair (http://www.iroothair.org/) | A comprehensive database of root hair genomics information | Kwasniewski et al. (2013) |
| SUBA3 (http://suba.plantenergy.uwa.edu.au) | Combines manual literature curation of large-scale subcellular proteomics, fluorescent protein visualization, and protein-protein interaction data sets from Arabidopsis with subcellular targeting calls from 22 prediction programs | Tanz et al. (2013) |
| Arabidopsis Interaction Viewer (http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi) | Queries a database of 70,944 predicted and 28,556 confirmed Arabidopsis interacting proteins against the protein(s) of interest; includes subcellular localization from SUBA | Geisler-Lee et al. (2007) |
| PlantMetabolomics.org (http://plantmetabolomics.vrac.iastate.edu/ver2/) | A National Science Foundation-funded multi-institutional project that is developing metabolomics as a functional genomics tool for elucidating the functions of Arabidopsis genes; the consortium has established metabolomic platforms that detect approximately 1,800 metabolites | Bais et al. (2010) |
| Ionomics Hub (http://www.ionomicshub.org/home/PiiMS) | Contains curated ionomic data on many thousands of plant samples (from Arabidopsis, Brassica napus, rice [Oryza sativa], maize, and soybean [Glycine max]) |