ReIN: An interactive tool to create and visualize regulatory networks in Arabidopsis thaliana

ReIN is a web-based software tool for creating, visualizing and identifying regulatory networks in Arabidopsis thaliana. Regulatory motifs represent the simplest units of the overall regulatory network of an organism. A simple graphical interface tool like ReIN will facilitate biologists a fast and easy way to visualize networks of interactions in Arabidopsis with the potential to be extended to other organisms.

A significant and unique feature of ReIN is that it displays different colors, shapes and variations for each object (TFs, Non-TFs, targets and its regulation type) in the network. TFs are represented as circles with lines connecting them to their targets. Lines with blue arrows indicate that the TF positively regulates the target, while lines with red arrows indicated the TF represses the target. By clicking on the arrows, the user can link to the papers in PubMed which documents the interactions. Non-TF targets (which can be any gene that encodes a product that does not act as a DNA-binding TF) are represented as rounded squares and are always the end of a given network motif. TFs and non-TFs are provided with dynamic links to its interactions. The users can save their work in graphical format

Key Features

Search – option finds and displays list of objects (nodes) based on id or a keyword

Interactions - when the user clicks (or double clicks in a MAC) the right bottom on any node (TFs) and chooses the “Protein-DNA interactions” option it searches the database and displays TFs or genes functionally linked to a selected node, enabling user ease in building the pathway.

Create – enables users to build custom networks with ability to add links to public repositories such as PubMed or The Arabidopsis Information Resource (TAIR, www.arabidopsis.org ). The user can also add interactions to the current visualization.

Import – receives input file in tab-delimited text format and automatically builds the network based on the imported data.

Layout – enables the users to zoom in/out and pan for browsing. It also enables users to drag and rotate the network. An additional option is provided to store the network as an image.

Portable –since it is a java based web-application, all the modules are portable and can be extended or integrated to other projects of similar nature.