Fig. 2: The user interface of PTMNavigator.

A The main interface of PTMNavigator. (1) Datasets can be accessed via a 32-digit Session ID that users receive during data upload. An arbitrary combination of datasets can be loaded at the same time. (2) A dataset may contain multiple experiments (specified in the uploaded CSV file). In this panel, experiments can dynamically be added to and removed from the diagram. (3) The list of pathways to choose from is sorted by scores from a gene-centric redundant enrichment analysis. Users can also search this list for the name or identifier of a pathway or filter for pathways that contain a specific set of genes or proteins. (4) Users can switch between a viewing mode, in which they can study the projection of their data onto pathway diagrams, and an editing mode, in which they can modify existing and create custom pathways. (5) The main canvas. After selecting a pathway, its diagram is rendered here. Additional smaller nodes are added for the peptides in the user data. (6) Initially, all peptides of a regulation group (up-/down-/unregulated) belonging to the same protein are summarized in one circular node labeled with the number of peptides it contains. Double-clicking on it allows a summary node to be expanded into individual nodes for each peptide (elliptical shapes). The position of the modified residue can optionally be displayed above the ellipsis. (7) All information supplied during the upload is displayed as a tooltip when hovering over a node. If a site is annotated in PhosphoSitePlus, a link to the annotation is retrieved. B The Enrichment Analyses View. Here, it shows the three most significant results from a Kinase-Substrate Enrichment Analysis (KSEA).