Table 1.
Plant transcriptome databases.
| Database | Plant species | Link | Reference |
|---|---|---|---|
| CROSS-SPECIES RESOURCES | |||
| Array express | ∼ | http://www.ebi.ac.uk/arrayexpress/ | Brazma et al. (2003) |
| Co-expressed biological processes (COP) | Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Hordeum vulgare, Zea mays, Glycine max, Triticum aestivum, Vitis vinifera | http://webs2.kazusa.or.jp/kagiana/cop/ | Ogata et al. (2009) |
| Gene expression omnibus (GEO) | ∼ | http://www.ncbi.nlm.nih.gov/geo/ | Edgar et al. (2002) |
| Genevestigator | Arabidopsis thaliana, Hordeum vulgare, Oryza sativa, Triticum aestivum, Nicotiana tabacum, Physcomitrella patens, Solanum lycopersicum, Zea mays | https://www.genevestigator.com/gv/ | Zimmermann et al. (2004) |
| NASCArrays | ∼ | http://affymetrix.arabidopsis.info | Craigon et al. (2004) |
| Stanford microarray database (SMD) | ∼ | http://smd.stanford.edu/ | Sherlock et al. (2001) |
| The botany array resource (eFP browser) | Arabidopsis thaliana, Populus trichocarpa, Medicago truncatula, Oryza sativa, Hordeum vulgare, Zea mays, Glycine max, Solanum tuberosum | http://bar.utoronto.ca/welcome.htm | Winter et al. (2007) |
| SPECIES-SPECIFIC RESOURCES | |||
| Arabidopsis transcriptome genomic express database | Arabidopsis thaliana | http://signal.salk.edu/cgi-bin/atta | Yamada et al. (2003) |
| CSB.DB | Arabidopsis thaliana | http://csbdb.mpimp-golm.mpg.de/ | Steinhauser et al. (2004) |
| Maize C3/C4 transcriptomic database | Zea mays | http://c3c4.tc.cornell.edu/search.aspx | – |
| Medicago truncatula gene expression atlas | Medicago truncatula | http://mtgea.noble.org/v2/ | Benedito et al. (2008) |
| PopGenIE | Populus trichocarpa | http://www.popgenie.org/ | Sjodin et al. (2009) |
| RiceGE | Oryza sativa (indica/japonica) | http://signal.salk.edu/cgi-bin/RiceiGE; http://signal.salk.edu/cgi-bin/RiceGE | Li et al. (2006), Liu et al. (2007) |
| RNA-seq atlas of Glycine max | Glycine max | http://soybase.org/soyseq/ | Severin et al. (2010) |
| Tomato expression database | Solanum lycopersicum | http://ted.bti.cornell.edu/ | Fei et al. (2006) |
| Transcriptome atlas of Glycine max | Glycine max | http://digbio.missouri.edu/soybean_atlas/ | Libault et al. (2010) |