Overview of the Abasy Atlas interface

Abasy Atlas has a hierarchical structure enabling users to browse through the available regulatory network models, their systems and systems-level elements. In every section of Abasy Atlas, a top menu bar displays five options and a search interface. The options are Homepage, Browse, Downloads, About, and Contact. Homepage is a shortcut to the homepage. Browse enables the user to explore through the atlas. Download displays an interface to download data as flatfiles. About provides background information on the atlas and the NDA. Finally, Contact provides a form for feedback from users. The Browse option and the search interface provide the two main ways to start exploring data contained in Abasy Atlas. They will be discussed in the following sections along with graphical browsing of regulatory network models.

Abasy Atlas is cross-linked to various external databases and sites providing biological, genomic, and molecular details. When a user visits an external database or site this opens in a new browser tab, whereas hyperlinks redirecting to other sections in Abasy Atlas open in the same tab.

Browsing Abasy Atlas

The Browse option is the entry point for browsing the whole atlas. This redirects to a section listing all the regulatory network models contained in the atlas. Each regulatory network model lists genome size, regulatory network genomic coverage, PubMed IDs of the data source, number and percentage of global regulators, modular genes, intermodular genes, and basal machinery genes, number of systems (modules) and a link to a separated section listing the global properties of the regulatory network model. From here, the user can list all the genes in the regulatory network model, retrieve a list of all the genes in a given class, or list all the identified systems.

In the list of genes, genes are listed along with their product description and the predicted class of system-level element (the latter only applicable for all and modular genes). Each gene name is canonical (see Construction and content section in our paper) and links to a gene details section showing identity (locus tag, UniProt ID, NCBI GeneID, and synonyms) and functional (product function, GO terms, and COGs) information on the gene along with their in-degree, out-degree and clustering coefficient, and an interactive network panel displaying the gene and their graph neighborhood (see Interactive network panel). Here the canonical gene name cross-links to specialized databases containing genomic and molecular details.

By following the modules link in the regulatory network models listing, the users get a list of all the systems identified in that regulatory network model. Data displayed in that list comprise the number of genes belonging to that system, the enriched GO terms and their q-value, and a module ID linking to another section displaying the system in an interactive network panel and listing the genes belonging to the system along with their product descriptions.

An interface to search Abasy Atlas is also available in the top menu bar of every section. Users may search a gene in all the regulatory network models (by default) or in a subset by selecting the proper option in a searchable dropdown list allowing multiple selections. Search using this interface is case-insensitive and the user may employ wildcards in the search string. Supported wildcards are ‘?’ to match any single character and ‘*’ to match any arbitrary number of characters including zero.

The search engine looks for the query in the set of canonical gene names, synonyms and locus tags returning a composite set of results grouped for each regulatory network model and ordered by canonical gene name (Figure 1). The results section lists all the matches found providing canonical gene names, NCBI GeneIDs, locus tags, UniProt IDs, synonyms, and classes of systems-level elements. Gene names link to the details section described above. If the class of systems-level elements is a system, this links to the corresponding entry in the list of all the systems identified in that regulatory network model.

Figure 1. Querying Abasy Atlas.

Interactive network panel

Abasy Atlas displays gene graph neighborhoods (i.e., the set of all the genes/complexes regulating or being regulated by a given gene, including the latter) and systems in interactive network panels that share a common interface (Figure 2). This interface provides a button to download an image in PNG format with transparency containing the network displayed, which is free for use in papers and other academic/non-commercial uses as long as proper citation is provided. It is also possible to remove global regulators, disconnected nodes, and weakly supported interactions temporally. A dropdown list enables the user to apply a layout to the network, and a button reapplies the selected layout. A checkbox controls if layout transitions are animated or not, this is a useful control when the number of nodes could slow the web browser. The full quality checkbox controls whether full quality is used during network manipulation and animated layout transitions. The animation is off by default, and we suggest this for improved responsiveness. The configuration of all the checkboxes and selected layout is preserved across a session in the same web browser tab. When the user closes the tab, the configurations are restored to default.

We fine-tuned the parameters for rendering the network in order to optimize responsiveness and user experience. Besides, we developed an adaptive layer running on top of the algorithms rendering the network. Before a network is rendered, this adaptive layer assesses the performance of the user’s computer and, if necessary, overrides user’s selections for a smoother experience. If the adaptive layer found that the user’s computer will exhibit degraded performance for a particular network, then layout animation is disabled and the network is always initially displayed using the grid layout despite previous user selections. The user can always re-enable layout animation or change the layout upon accepting a warning regarding the risk of degraded performance.

In the upper-right corner of the network panel, a widget similar to that used by Google Maps is available. This widget enables panning and zooming the network. The user may also use the mouse wheel for zooming the network. Inside the interactive panel, the network is displayed by using a color code for nodes and interactions. We encoded interaction effects in line colors and arrowhead shapes as follows: red and T shape for repressions, green and arrow shape for activations, orange and diamond shape for dual, and grey and arrow shape for unknown effect. Evidences supporting interactions, if available, are encoded as different line styles: solid for strong evidences and dashed for weak evidences. Genes belonging to the same system or class of systems-level element have the same color. In the gene details section, the central gene is highlighted in yellow. If the central gene product is a subunit shared by several complexes, all these complexes are also highlighted. We represented heteromeric regulatory complexes as pentagons, whereas genes are circular nodes.

All the nodes can be draged around and repositioned, and clicking on an interaction switches its state between normal and highlighted. If the mouse hovers over a node or interaction, a tooltip displays providing information such as local (neighborhood dependent) out- and in-degrees, subunits if the node is a regulatory complex, and links to other genes and systems. The user also may explore the regulatory network model by graphical browsing. If the user clicks in a node, he is redirected to the details section of the corresponding gene.

Figure 2. Interactive network panel for module 1.19 of our meta-curation of B. subtilis 168.