SLiMScape, a Cytoscape plugin, is a platform for performing short linear motif analyses of protein interaction networks by integrating motif discovery and search tools in a network visualization environment. This aims to aid in the discovery of novel short linear motifs, as well as visualisation of the distribution of known motifs.
This readme gives an overview of the key SLiMScape features. More information can be found at the SLiMScape GitHub wiki and the SLiMSuite blog.
To install, simply navigate to the Cytoscape App Store and click the install button. This will add the app to your local Cytoscape version.
The minimum input for SLiMScape is an interaction network which contains a Uniprot attribute for each node OR a run ID from the UNSW servers. At the moment, the name of the node needs to be its Uniprot ID or Accession Number for the server to know what to do with it.
An example input with Uniprot IDs is:
| name |
| P54253 |
| O35147 |
| Q61337 |
| P04049 |
| Q99683 |
| Q9EPK5 |
An example input with a run ID is:
| Run ID: | 15020400003 (SLiMProb run) |
SLiMProb will also need query motif input in the form of regular expressions (see FAQs for details).
Once a search has been completed, the nodes that contain SLiMs will change from the default blue circles to red diamonds. The rest of the nodes will remain as they were.
If you want to pre generate a job on the Slimsuite servers, you can do that from here. If you do this, you can input the generated run ID to Cytoscape, and a graph will be generated for you! It's also handy for larger jobs that may take a while to finish.
A run will produce both graph changes, and a results panel.
In the graph, nodes possessing SLiMs will become red diamonds; if a node has more than one SLiM it will be a daker shade of red. Note that there is not currently a layout set automatically, and the user will have to go to the layouts tab at the top of the page, and select one from there in order to see all of the nodes.
Results for SLiMProb are displayed in two panels.
Main Results Panel contains:
- Motif: The name of the motif.
- Pattern: The motif definition.
- IC: Information content.
- N_Occ: Number of specified SLiM occurrences.
- N_Seq: Number of nodes the SLiM occurred in.
- N_Upc: Number of nodes in the unrelated protein cluster (UPC).
- E_Upc: Enrichment score for the unrelated protein cluster.
- p_Upc: Significance value of the unrelated protein cluster.
- pUnd_Upc: Probability of seeing the observed number of occurrences or less of the UPC.
OCC Panel contains:
- Motif: The motif found in the sequence.
- Seq: The name of the sequence.
- Start_Pos: The start position of the sequence.
- End_Pos: The end position of the sequence.
Results for SLiMFinder and QSLiMFinder are displayed identically, also in two panels:
Main Results Panel contains:
- Rank: Rank of the motifs found, from most to least common.
- Sig: Motif significance value.
- Pattern: Regex of the motif found.
- IC: Information content of the motif.
- OCC: Enrichment score for the occurence(s).
- Support: Number of sequences the motif occurs in (no distinction made between motifs with multiple occurences).
- UP: Unrelated proteins the motif occurs in.z
OCC Panel contains:
- Pattern: Regex of the motif found.
- Sig: Motif significance value.
- Seq: The name of the sequence.
- Start_Pos: The start position of the sequence.
Further results can be obtained on the internet, at the URL: http://rest.slimsuite.unsw.edu.au/retrieve&jobid={jobid produced when the run is performed}. Alternatively, there is a button at the bottom of the results panel which will open the above link in your browser.
SLiMProb searches the protein sequences of the selected nodes for occurrences of a specified regular expressions; useful for locating new instances of a motif found using SLiMFinder (e.g. R[SFYW].S.P). Conventions as used in the program can be found here.
SLiMProb has one input; a SLiM to be searched for in the nodes selected on the graph. To run SLiMProb you must provide a regular expressions in the motifs box and select one or more nodes. Alternatively, if you know the run ID of a previous search, you can instead input that to the Run ID textbox.
If the motif is found, the colour and shape of the target node will change.
Masking
- Disorder Masking is used to mask residues which have an IUPred disorder score of less than 0.3
- Conservation Masking is used to mask residues which have a relative local conservation score of less than X.
Custom Parameters
- Custom parameters can be used to add other command line arguments which can be found here.
##SLiMFinder SLiMFinder aims to discover new motifs in the selected protein interaction network by searching for statistically overrepresented sequences within a set of proteins.
It has no mandatory inputs other than a selection of graph nodes or a run ID. If a motif is found in a node, the node will change colour and shape. The specific motif is presented in an output table, along with the Uniprot ID and other data.
Masking
- Disorder Masking is used to mask residues which have an IUPred disorder score of less than 0.3
- Conservation Masking is used to mask residues which have a relative local conservation score of less than X.
- Feature Masking is used to mask residues which occur in features such as domains or transmembrane regions.
SLiMBuild
- Maximum SLiM length lets the user set the maximum length of SLiMs to return.
- Maximum consecutive wildcards allows the user to alter the number of wildcards to return.
- Ambiguous motifs either allows or disallows the returning of ambiguous motifs.
Miscellaneous Options
- Custom parameters is used to add other command line arguments which can be found here.
QSLiMFinder is a modification of SLiMFinder, aimed at looking for SLiMs shared by a query sequence and one or more additional sequences. SLiMs are drawn from the "Query" sequence, then searched for in the other nodes in the set.
QSLiMFinder requires a "Query" input; the Uniprot ID or Accession Number for the node you'd like to get your SLiMs from. This node does not have to be present in the graph. If a motif is found in a selected node, the node will change colour and shape. The specific motif is presented in an output table, along with the Uniprot ID and other data.
Masking
- Disorder Masking is used to mask residues which have an IUPred disorder score of less than 0.3
- Conservation Masking is used to mask residues which have a relative local conservation score of less than X.
- Feature Masking is used to mask residues which occur in features such as domains or transmembrane regions.
SLiMBuild
- Maximum SLiM length lets the user set the maximum length of SLiMs to return.
- Maximum consecutive wildcards allows the user to alter the number of wildcards to return.
- Ambiguous motifs either allows or disallows the returning of ambiguous motifs.
Miscellaneous Options
- Custom parameters is used to add other command line arguments which can be found here.