My Pathways

Use My Pathways to create customized pathways for your targets, biomarkers, processes, and diseases of interest. In addition, integrate your proprietary biological and chemical relationships into IPA pathways. Many different options exist for creating a new pathway, e.g. add one molecule at a time or add molecules from a list to the diagram. Follow the steps below to learn how to use this feature.

 

A new pathway can be created by selecting molecules in various views and clicking on the Add To Pathway button. You can create custom Pathways from the following locations:

 

  • Lists

  • Search results*

  • Functional Analysis

  • Networks


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*Adding molecules to a pathway from a search result, an option will be available to add the molecules or targets to the pathway. Use the Add Molecules option if you want to add the actual search results to the pathway. Use the Add Targets option if you want to add the targets of a drug or chemical.

 

You can also create Pathways from scratch by using the Add Molecule/ Relationship features in IPA, or by dragging and dropping molecules from another pathway, list, or annotations table.

 

Saving My Pathways

Once you have completed all the modifications on your My Pathway, save it by clicking the User-added image  icon. This My Pathway will be saved in the project folder that you choose, as well as in the My Pathways Library in the Project Manager.

 

Sending My Pathways by E-mail

From an open My Pathway, click the User-added image  icon to send an interactive pathway diagram to a colleague. Fill in the e-mail address and click the OK button.


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Approving My Pathways


Each pathway either has a status of "Approved" or "Not Approved". Once approved, My Pathways will be made available for My Pathways analysis as well as My Pathways overlay for individual networks. As a default, My Pathways are NOT approved. However, you can approve a My pathway in one of two ways:

 

1) While saving a pathway, check the Approve this Pathway for use in my analyses box.


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2) Alternatively, if you want to approve a My Pathway later on, you can go to the Project Manager, then open the My Pathways Library, and right-click on the pathway whose approval status you want to alter. Then select Approve from the dialog box that appears, as shown below. You can also change the status of an Approved My Pathway later on, by following the same steps, except select "UnApprove" from the dialogue box.

3) You can now approve a WHOLE folder of My Pathways in one click.  Choose the My pathway Folder you want to approve, right click and then select  Approve all Pathways . Choose Un Approve all Pathways if you would like to change the status of all approved pathways in that folder. 

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My Pathways Analysis


Once a Pathway has been created, saved, and approved, you can score it against any analysis that you upload. While running the analysis on the create analysis page, in the General Settings, but a check in the box for  My Pathways.


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All approved My Pathways are available from the My Pathways tab once an analysis has been run and opened.  Approved My Pathways are scored against your input file for every analysis you run, regardless of whether the analysis is run in your own workspace or under the Projects Shared with Others folders.  My Pathways located in the Projects Shared with Me folder will not be scored against your analyses, even if they have been approved.  Custom nodes that are part of a My Pathways will not be taken into consideration during the scoring process.

 

The scores of the My Pathways are displayed as a bar chart. The x-axis displays the individual My Pathways and the y-axis displays the ratio. The ratio reflects the number of Functions/Canonical Pathways Analysis molecules relative to the total number of molecules that map to the My Pathway.

 

The chart for My Pathways analysis can be customized by clicking "Customize Chart". The style of the chart can be altered by clicking the "Bar Chart" or "Line Chart" buttons.

 

Single clicking on a bar from the My Pathways chart displays the molecule details for the molecules involved in that My Pathway. To view detailed information for each molecule in the pathway, click on the molecule symbol in the name column and this will open a Gene or Chemical View window for that molecule.

 

My Pathway Reports

My Pathway Reports show a variety of detailed information about each My Pathway within your IPA workspace. Pathway Reports are also available for Path Designer Pathways.

 

  • You can access the My Pathway report by double clicking on a bar from the Pathway bar chart from within an analysis, and then clicking "View Report". Alternatively, you can access the My Pathway report by finding the My Pathway in the Project Manager, and right clicking on it.


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  • Clicking the title at the top of the My Pathway Report will open the My Pathway diagram.

  • The time stamp displays the time the report was generated.

  • The Top Functions displays a local functional analysis of all the molecules within the pathway. The top three high-level functional categories are displayed here.

  • The Molecules section lists the molecules within the Pathway. Clicking the links opens the Gene or Chem View for the molecule.

  • The Drug Summary displays an overview of the drugs that target molecules on the pathway. The Preview setting displays the first 3 drugs. Click Show All to display all.

    • This table can be resorted by clicking on the column header row.

    • For Indications and Status, the first 3 alphabetical indications/ status are displayed.

  • The Targets section displays an overview of any genes that are targets of drugs within the Pathway.

    • This table can be resorted by clicking on the column header row.

  • The references section is based on the relationships present within the Pathway and the Findings that support the relationships.

  • Any changes made to a pathway must be saved before the Pathway Report will be updated.

  • My Pathway Reports can be exported as interactive PDF files by clicking the User-added image  button.