Table 2.
Web resources for plant networks.
| Network | Species | Link | Standards | Reference |
|---|---|---|---|---|
| GENE-REGULATORY NETWORKS | ||||
| AGRIS | Arabidopsis thaliana | http://arabidopsis.med.ohio-state.edu/REIN/ | CSV* | Yilmaz et al. (2011) |
| Regulog | Arabidopsis thaliana | http://interolog.gersteinlab.org | CSV* | Yu et al. (2004) |
| RIMAS | Arabidopsis thaliana | http://rimas@ipk-gatersleben.de | SBGN GML | Junker et al. (2010) |
| METABOLIC NETWORKS | ||||
| KEGG | Arabidopsis lyrata, Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Ricinus communis, Sorghum bicolor, Vitis vinifera, Zea mays | http://www.genome.jp/kegg/pathway.html | KGML | Ogata et al. (1999), Kanehisa et al. (2010), Kanehisa et al. (2012) |
| MetaCrop | Arabidopsis thaliana, Beta vulgaris, Brassica napus, Hordeum vulgare, Medicago truncatula, Oryza sativa, Solanum tuberosum, Triticum aestivum, Zea mays | http://metacrop.ipk-gatersleben.de/ | SBML SBGN GML | Schreiber et al. (2012) |
| PANTHER | Arabidopsis thaliana, Oryza sativa Japonica | http://www.pantherdb.org/pathway/ | SBGN BioPAX | Mi et al. (2010) |
| PlantCyc | Arabidopsis thaliana, Brachypodium distachyon, Oryza sativa, Populus trichocarpa, Sorghum bicolor, Zea mays | http://plantcyc.org/ | BioPAX | Caspi et al. (2006) |
| Reactome | Arabidopsis thaliana, Brachypodium distachyon, Glycine max, Medicago trunculata, Nicotiana tabacum, Oryza sativa, Populus trichocarpa, Sorghum bicolor, Vitis vinifera, Zea mays | http://www.reactome.org/ | SBGN SBML BioPAX | Croft et al. (2011) |
| Wiki pathways | Arabidopsis thaliana, Oryza sativa, Zea mays | http://www.wikipathways.org | BioPAX | Kelder et al. (2012) |
| CO-EXPRESSION NETWORK | ||||
| AraNet | Arabidopsis thaliana, Hordeum vulgare, Oryza sative, Populus trichocarpa, Triticum aestivum, Medicago truncatula, Glycine max | http://aranet.mpimp-golm.mpg.de/aranet/ | CSV* | Mutwil et al. (2010, 2011) |
| AGCN | Arabidopsis thaliana | SIF | Mao et al. (2009) | |
| atGGN | Arabidopsis thaliana | http://bioinformatics.cau.edu.cn/atGGN/ | WWW | Ma et al. (2007) |
| @CoEX | Arabidopsis thaliana | http://ibis.tau.ac.il/AthMod/ | WWW | Atias et al. (2009) |
| ATTED-II | Arabidopsis thaliana, Oryza sativa | http://atted.jp | CSV* | Obayashi et al. (2009), Obayashi et al. (2011) |
| Gene co-expression network browser | Maize, rice | http://www.clemson.edu/genenetwork/network.php | WWW | Ficklin and Feltus (2011) |
| Co-expressed gene network in barley | Hordeum vulgare | http://coexpression.psc.riken.jp/barley/index.pl | CSV* | Mochida et al. (2011) |
| PROTEIN–PROTEIN-INTERACTION NETWORK | ||||
| AtPIN | Arabidopsis thaliana | http://bioinfo.esalq.usp.br/atpin | SIF | Brandao et al. (2009) |
| Biogrid | Arabidopsis thaliana, A. lyrata, Brachypodium, Glycine max, Oryza sativa, Populus trichocarpa, Sorghum bicolor, Zea mays | http://thebiogrid.org/ | CSV* | Stark et al. (2006) |
| IntAct | Arabidopsis thaliana, Oryza sativa | http://www.ebi.ac.uk/intact/ | CSV* | Kerrien et al. (2012) |
| Interolog | Arabidopsis thaliana | http://interolog.gersteinlab.org/ | CSV* | Yu et al. (2004) |
| iRefIndex | Arabidopsis thaliana, Arachis hypogaea, Artocarpus heterophyllus, Artocarpus integer, Canavalia ensiformis, Glycine max, Hordeum vulgare, Nicotiana tabacum, Oryza sativa, Oryza sativa Japonica, Petunia x hybrid, Pisum sativum, Solanum lycopersicum, Spinacia oleracea, Triticum aestivum, Zea mays | http://irefindex.uio.no/wiki/iRefIndex | CSV* | Razick et al. (2008) |
| MiMI | Arabidopsis thaliana, Oryza sativa Japonica | http://mimi.ncibi.org/MimiWeb/main-page.jsp | CSV* | Jayapandian et al. (2007) |
| PAIR | Arabidopsis thaliana | http://www.cls.zju.edu.cn/pair/ | CSV* | – |
| Pathway commons | Arabidopsis thaliana | http://www.pathwaycommons.org/pc/home.do | BioPAX SIF | Cerami et al. (2011) |
| String | Arabidopsis lyrata, A. thaliana, Brachypodium distachyon, Oryza sativa Indica Group, O. sativa Japonica Group, Populus trichocarpa, Sorghum bicolor, Vitis vinifera | http://string-db.org | WWW | Szklarczyk et al. (2011) |
| SIGNAL TRANSDUCTION PATHWAYS | ||||
| PANTHER | Arabidopsis thaliana, Oryza sativa Japonica | http://www.pantherdb.org/pathway/ | SBGN BioPAX | Mi et al. (2010) |
| Pathway commons | Arabidopsis thaliana | http://www.pathwaycommons.org/pc/home.do | BioPAX SIF | Cerami et al. (2011) |
| Wiki pathways | Arabidopsis thaliana, Oryza sativa, Zea mays | http://www.wikipathways.org | BioPAX | Kelder et al. (2012) |
*Requires preprocessing in order to get a network for upload in HIVE, WWW indicates webresources without the possibility for download of network files.