1. Aidan Tay Avatar Aidan Tay
  2. Proteomics
  3. PTMOracle

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PTMOracle / Quick_Start

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Quick Start

This page describes a quick way to get started with using PTMOracle. For a more detailed explanation or description of how to use the PTMOracle, please refer to the User Manual.

Initialisation

  1. Ensure the correct version of Cytoscape is installed. PTMOracle requires minimum of version 3.1 of Cytoscape to work.

  2. Install PTMOracle from the app store.

  3. Create the example yeast interactome (Apps -> PTMOracle -> Examples -> Yeast Interactome).

  4. Download the XML-based files required by PTMOracle from the publication supplementary files (Supporting Information 2) and unzip the contents.

  5. Import yeast PTMs (yeast_uniprot_dbptm_proteomescout_ptms.xml) into Cytoscape using the PTMOracle import menu (Apps -> PTMOracle -> Import...). Ensure that you have selected UniprotAcc as the mapping column and entered PTMs as the source. Importing data may take some time to run.

  6. After importing PTMs, import yeast protein sequences (yeast_uniprot_sequences.xml) into Cytoscape using the PTMOracle import menu. Ensure that you have selected UniprotAcc as the mapping column and entered Sequences as the source.

Visualising PTMs

  1. If not already shown, show the Cytoscape Control Panel (View -> Show Control Panel).

  2. Select the OraclePainter tab in the Cytoscape Control Panel to reveal the colour palette. Click Apply to paint protein nodes as pie charts. Each section in the pie chart represents a PTM type and its frequency as a proportion of the total number of PTM sites on the protein node. Feel free to move around, zoom and explore the network.

Displaying PTMs

  1. Using the Cytoscape search bar, look for the YBR059C protein.

  2. Show all columns in the Cytoscape Table Panel.

  3. If not already shown, show the Cytoscape Results Panel (View -> Show Results Panel).

  4. Select the OracleResults tab in the Cytoscape Results Panel to reveal a text box.

  5. Input the SUID of the YBR059C protein into the text box of OracleResults. Click View to examine all the PTM sites mapped onto the YBR059C protein. The protein sequence for the YBR059C protein will also be shown and highlighted with PTM sites (as pink).

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