Drugst.One

The detail view shows the node information of the currently selected network component. The name and the group of the gene will be displayed here. If a gene can be found in Drugst.One’s database, results will be complemented by information retrieved from different databases. If a tissue is selected, the exact measured expression value will be displayed here when the gene is selected. If the gene can be found in the Drugst.One database and is thus available for selection, a button to toggle the selection status for the gene will be displayed.

The overview panel shows a summary of the currently displayed network with the number of edges and nodes.

Use this panel to search for specific nodes in the network. The search bar filters the nodes in the network and has a useful autocomplete function. The query functionality is especially valuable when exploring large and complex networks.

This panel connects the genes in the network with just one click. It starts a Multi-Steiner algorithm for all genes in the network (or just the ones that have been selected). The resulting network finds connections between the seed genes if any do exist.

This panel searches for drug candidates with just one click. First, it starts a Multi-Steiner algorithm on all genes in the network (or just the ones that have been selected). Second, it prompts Drugst.One to execute a Closeness Centrality algorithm on the resulting network to find drug candidates that are related to the original seed genes.

The analysis panel gives the user three ways to analyze the selected seed genes. Drug target search selects algorithms that will find genes related to the seed genes. Depending on the selected algorithm, it will either try to find genes in between the seed genes or search for new genes in close proximity to the seed genes. These genes can either extend existing the disease module or, if considered in the context of drug repurposing, represent putative drug targets. Drug search works in a similar manner, but in this case the algorithms will return a list of putative drugs in the network neighborhood of the seed genes. Enrichment analysis will export the list of selected genes either to g:Profiler or DIGEST to offer different evaluation, enrichment, profiling and conversion methods. You can also search for selected proteins in NDEx integrated Query (iQuery) to show curated pathways with the same participants.

This list provides an overview of active tasks and indicates: the algorithm used, the task status (‘running’, ‘done’, ‘failed’) and a timestamp for each of them. Tasks are listed chronologically, from newest to oldest. Clicking on a specific task opens up the analysis window for it. Tasks that are not relevant anymore can be deleted by the user, either individually or all together by clicking on ‘Delete All’ at the bottom of the list.

This panel shows a list of all selected genes, displaying both their labels and group. Individual genes (or the complete selection) can be removed from here. Genes can be manually selected by double-clicking nodes in the network, checking boxes in the tabular view, or just by using the ‘rectangular select’ function (pressing shift and holding the left mouse button down while dragging the cursor over the network). Options for selection expansion are provided though the ‘Add First neighbors’ and ‘Add Connected Components’ buttons, which use the current selection list as input.

This panel shows a list of all created views. A view is a subnetwork based on a selection of other networks. A new view can be created and displayed in the network panel by selecting a network and a selection of genes within it. Views can also be deleted from the list. The view list is saved in the browser’s local storage and will be restored when you return to the page.

The network menu manages all options that are directly related to the network. It allows you to modify the network, add and remove node types and highlight genes based on expression: Reset View resets the network zoom and center the network, Screenshot exports the network as an image. Download downloads the network data as .graphml, .json or .csv, Tissue visualizes the expression information for genes in the network based on GTEx media Tissue expression (TPM) values, Drugs displays first neighbor drugs for the genes in the network, Disorders (Protein) displays first neighbor disorders for the genes in the network, Disorders (Drug) displays first neighbor drugs for the disorders in the network, Animation toggles the network physics (on/off), and Seeds (only available in analysis mode) highlights the seeds used for the analysis in the network.

If there are selected genes in the network, Drugst.One can be used to execute network algorithms based on them. Algorithms can be run in the sidebar Analysis panel. There, you can choose between drug and drug target searching algorithms, and configure a number of different parameters to customize the algorithm to your needs. Alternatively, the Quick Drug Search and the Connect Genes panels in the sidebar can be used to run predefined algorithms.

This window can be opened by clicking on finished tasks in the task list on the sidebar, and consists of three different tabs: Table contains all the data used for the analysis and displays the genes/proteins of the search and the ones found by the algorithm. If applicable, an additional table ranks the found drugs. Network shows the resulting network in the analysis context, displaying the complete input network such that the found nodes can be interpreted in its context. The network menu in the analysis view can highlight the used seed nodes for the analysis task, hence the genes which the algorithm received as input. In addition to the initial network, the analysis network contains additional node groups for the found nodes (‘foundNodes’) and for possible connectors (‘connectorNode’). Parameters contains all information needed to reproduce the results. Here you can find the name of the used algorithm, the version numbers of the used datasets and the additional parameters that were set.