SIGNOR 2.0 offers several options to browse its content:

1. Basic Entity Search: directly type a protein/gene name or other entity identifier and click the search button. This can also be achieved by using the quick-search box in the top menu.

Result Selection: when searching for genes, proteins, chemicals etc., the results page displays the list of entities whose names, synonyms or description matches the search term. In case of ambiguity, you are asked to pick the result you are interested in and click "Get Relation"(see below).

Preview Box: a preview box is displayed next to the list of results. By hovering on any of the results it is possible to view more detailed information about the entity in order to make the selection more accurate (see below).

Entity Page: after searching for an entry or clicking on an entity in the interactive graph, the Entity Page is loaded (see below).
This page shows details about the selected entity including:

1. General information such as Gene Name, Synonyms, links to UniprotKB and Protein Function
2. Interactive Graphic Visualization of the selected entity and its interactors. Nodes and edges are clickable.
3. Manually annotated modifications, if any, including sequence, modifier and other details.
4. Causal relationships listed in a tabular format. Supporting evidence is listed and sample sentences are reported.
5. Extra information about modifications, organisms and links to supporting papers, accessible by pressing the "+" button next to each relation.
6. Search tool box allows to refine the search by filtering for a specific mechanism, effect, organism, etc.

2. Multi-protein Search: Allow the user to visualize networks at different level of complexity by entering a list of entity identifiers and selecting "all" to see all the interactors of the listed entities, or "connect" to retrieve a graph displaying only the interactions among the proteins in the list.

‘ALL’ Button

 ‘All’ button allows access to signaling interactions involving any of the seed entities and all the remaining proteins in the SIGNOR network without any further filtering.

‘Connect’ Button

The ‘Connect’ button searches for signaling interactions involving only any two entities in the query list.

First Neighbors’ Button

The ‘First Neighbours’ button is a multi-step strategy that initially performs a search in SIGNOR for all interactions involving any of the seed entities, next prunes nodes with degree one.

The “Searched Entities box” allows the user to select ‘edit nodes’ to consult and edit the list of the seed entities, by removing or adding nodes. By clicking on ‘Download Relations’ it is possible to download all the interaction displayed in the viewer.

‘Shortest Path’ search

This functionality allows the user to look for network paths linking two entities present in SIGNOR 2.0 (e.g. proteins, phenotypes, etc). The query could require a matter of tens of seconds, as the graph algorithms explore a variety of paths in the network.

Results are displayed as a graph and listed in a table . The figure below shows the result page of a sample query looking for functional connections between the protein EGFR and TP53.

The results page displays a graph showing the shortest path(s) linking the selected entities. The query entities are highlighted in red in the graph and the resulting network displays all the connecting paths of minimal length. Each row of the summary table contains the following information path:

• Path query: EGFR → TP53
• Path string: each step is characterized by two nodes and an edge, the edge can have four different symbols according to type of relation effect.

• → activation
• -| inhibition
• -[] form complex
• -? unknown effect

• Distance: this parameter provides an estimation of the path length where the reliability of each step is taken into consideration. Each single path step is associated to a reliability score r, taking into consideration a number of supporting evidence. The reliability score is converted into a distance by the following simpler relation:

 d = 1-r

The final path score is the sum of each step distance :

where N is the number of steps in a path

• Length: Number of steps in the path.

Depending on the even or odd number of inhibition steps, each path can be predicted to be activating or inhibiting for the target entity. This is represented in the table as a green or red background of the corresponding row. Whenever the path contains a relationship of unknown effect, the row is marked with a grey background.

3. Pathway Browser: select a pathway from any of the dropdown menus and press the button next to it to view information about it and a graph of the interactions that belong to it.

   Pathway Page:

Pathways are manually curated and the number of entities considered in each pathway is arbitrarily limited to the ones that are considered central in order to have an interpretable graph. Each edge and entity is clickable to get more information.
Entities are automatically laid out and assigned to specific cell compartments (extracellular space, membrane, cytoplasm, nucleus).
"Stimuli" and "Phenotypes" are always placed upstream and downstream respectively. A series of filters at the top of the graph frame allow the user to modify the display of the pathway by including or excluding indirect interactions or relationships below a score threshold.
It is possible to add entities from the visualization by using the dedicated box and subsequently remove them if so chosen. By clicking on ‘Download Relations’ it is possible to download all the interactions of the selected pathway.

4. Search by organism

SIGNOR 2.0 relationships are automatically mapped onto the human proteome and then remapped by orthology onto the proteome of the model organisms mouse and rat.  In the home page, on top of the main search box, users can select the preferred organism (human, mouse or rat). 

5. Search by PMID

Users can search interactions related to a specific paper by typing the PMID of the paper.
The result page will show information about the article and the curated interactions extracted from that specific paper.

6. Using the graphic visualizer

The graphic visualizer in an interactive graph viewer, where nodes are proteins (or other entities considered in SIGNOR) and edges illustrate the causal relationships between them. The graphic visualizer yields a dynamic, customizable display of the retrieved interactions, whose attributes are summarized with the use of symbols and color codes: direct interactions are displayed as solid lines and indirect ones as dashed lines, while edge color and arrow shape represent the effect (up- or down-regulation): up-regulations are represented as blue arrows, while down-regulations as red ‘T-shaped’ arrows. Nodes also have a color and shape code. The nodes that are used to query the SIGNOR database and retrieve the interactions that form the graph are small dark-green circles, while first neighbours are light green . White circles and blue clover leaves represent protein families and complexes respectively. Yellow squares represent small molecules and chemicals, while phenotypes and stimuli are rectangles.
Proteins, small molecules, stimuli, phenotypes and other entities are spatially organized in four main cellular compartments: extracellular space, plasma membrane, cytoplasm and nucleus, according to their manual annotation. Nodes can be manually moved by the user to obtain a customizable layout of the entities. Every relationship is linked to a score.

After clicking on a node a pop-up window displays the entity details: name, external accession number (e.g. UniprotAC, PubchemID), chemical inhibitors and link to the related SIGNOR page (See below).

By clicking on each edge it is possible to obtain details about the interaction: the mechanism (e.g. phosphorylation, binding…), the cell line or organism in which the interaction has been observed, the reference and the sentence supporting the interaction. Furthermore, it is possible for the user to evaluate the annotated relationship by clicking the green tick symbol (yes) or the red X symbol (no) to the question “Do you trust this relation?”, the feedback is used by curators to re-evaluate that specific annotation.

By clicking on symbols on the upper bar of the visualizer it is possible:

1. take a screenshot of the graph;
2. download data underlying the graph representation;
3. show or hide the interaction score;
4. show or hide the graph legend;
5. filter the type and the effect of the interactions or include/hide small molecules or chemical compounds;
6. select an edge score threshold;
7. select a type layout among ‘compact’ (where nodes are in close proximity), ’moderate’ and ‘relaxed’ (where nodes are more far apart) layouts;

7. Download Page

SIGNOR 2.0 data can be freely downloaded.

In the download page, the user can choose to download all dataset or a subset of data (i.e phosphorylation data, transcriptional relations, a specific pathway, etc) and in different formats, such as tab-delimited format, PSI-MI CausalTab, SBML and GMT.  Detailed information on CV and SIGNOR 2.0 entity data is available for download as well.

7. User Feedback

On the top left of the home page, there is a window that allows users to send any feedback to SIGNOR curators or developers. User feedback on SIGNOR 2.0 functionality or annotation quality is very much appreciated because it allows us to improve the quality of our resource. Moreover, we encourage users to suggest papers to curate or to send us their data prior to publication. Data privacy policy will be maintained prior to final publication.