TABLE 1.
Selected correlation network databases and tools.
| URL and comments | |
|---|---|
| Correlation network DB | |
| ATTEDII (Obayashi et al., 2009) | http://atted.jp/; explore condition-independent coexpression networks for up to 100 genes in Arabidopsis using the NetworkDrawer tool. Coexpression analyses may also be performed for rice. |
| CressExpress (Srinivasasainagendra et al., 2008) | http://cressexpress.org; generate condition-independent coexpression analyses or custom condition-dependent coexpression analyses for Arabidopsis with up to 30 genes. Results are easily imported into Cytoscape for visualization. |
| PlaNet (Mutwil et al., 2011) | http://aranet.mpimp-golm.mpg.de/; use this tool to explore condition-independent coexpression networks in seven plant species. Networks are displayed as static SVG images, but networks may also be downloaded for easy viewing and further manipulation in Cytoscape or Pajek. |
| CSB.DB (Steinhauser et al., 2004) | http://csbdb.mpimp-golm.mpg.de/; use this tool to explore both condition-independent or condition-dependent coexpression networks in Arabidopsis for up to 60 genes. Networks may be immediately viewed as images, or downloaded for further manipulation into the visualization tools below. |
| GeneMANIA (Mostafavi et al., 2008) | http://genemania.org/; this tool allows functional network generation in Arabidopsis based on user-selected or default expression data sets, protein–protein interactions, subcellular localization, shared protein domains, etc. Results are easily visualized via an embedded Cytoscape Web (Lopes et al., 2010) application. |
| SeedNet (Bassel et al., 2011) | http://bree.cs.nott.ac.uk/arabidopsis/; explore condition specific (i.e., seed-expressed) gene networks from Arabidopsis in a custom network explorer. |
| AraNet (Lee et al., 2010) | http://www.functionalnet.org/aranet/; like GeneMANIA this tool allows functional network generation in Arabidopsis. Results may be visualized via activation of Cytoscape Web. |
| Network visualization tools | |
| Cytoscape (Shannon et al., 2003; Kohl et al., 2011) | http://www.cytoscape.org/; use this powerful open-source desktop tool to visualize coexpression and other networks, such as those generated by protein–protein interaction studies. Nodes and edges may be appended with additional, user-defined information. |
| Biolayout (Theocharidis et al., 2009) | http://biolayout.org/; the current iteration of this desktop tool, Biolayout Express3D, permits visualization of coexpression and other networks in three-dimensional space. Cytoscape “.sif” files may be imported into the tool. |
| Pajek (Batagelj and Mrvar, 1998) | http://pajek.imfm.si/doku.php |