<b>PleioNet</b>

Upload a list of SNPs (optional)

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Choose levels to display

SNP

Gene

Disease/Trait

Parent Term

Genes

Diseases/Traits

Log:

Plot
Summary

Summary Details

PleioNet: Where connections are revealed.

PleioNet is a web-based visualization tool that may be used to explore the pleiotropic information of human diseases and traits in an intuitive and interactive manner. It is user-friendly and using it is as simple and easy as browsing a website.

The default interface shows the results for a five-SNP example dataset. An example interface is shown in the following figure. The numbers in this image correspond to the order of the manual.

Choosing Which Levels to Display ①
The user may select which levels to display in the network corresponding to his or her desired level of specificity. The default setting displays pleiotropic network results for the gene CDKN2B-AS1.

To include a level in the network visualization, check the box next to the desired level. To remove a level, uncheck the box next to the corresponding level. The network should adjust to the changes automatically.

Making Specific Gene and Trait Selections ②
The user may select a specific gene or multiple genes to investigate using the input options. Click on the input toolbar to type, or use the scroll down options to select. After a selection has been made, click on the submit button to update the displayed network. The input for diseases/traits operates in the same way.

Submit Button ③
After making a new selection for genes and/or diseases/traits, click on the “Submit” button to update the displayed network.

Plot and Summary Tabs ④
The Plot Tab shows the pleiotropic network designated by the selections on the left panel. Yellow, green, orange, and pink denote SNPs, genes, disease/traits, and parent terms, respectively. The arrows connecting the nodes point in the direction of decreasing specificity. Node size is proportionate to the number of connections that node has in the Genome Wide Association Studies (GWAS) catalog database.

The plotted figure can be maneuvered in a number of ways:

a) Zooming in and out
Hover the mouse over the pleiotropic network and drag two fingers across the mousepad (or use the scroll wheel on the mouse) towards or away from the user.

b) Highlighting a specific node and its connections
Use the mouse to hover over or click on the desired node on the homepage. This will gray out the other unrelated nodes, thus emphasizing those that are relevant within the selected network. To remove this selection, click elsewhere on the page.

An example is shown in the following figure with the “intraocular pressure measurement” node being clicked on.

c) Relocation
To move an entire network, click on the white space surrounding the network and drag to the desired location. To move a node, click on the selected node and drag to the desired location. The node may revert back to its original location after you stop clicking on it, depending on how the algorithm automatically balances the rendering.

The Summary Tab allows access to a summary table of pleiotropic network results. Users may use the search bar in the top righthand corner of the page to isolate or group results as needed. Users can also click on the SNPID and PUBMEDID to get more detailed GWAS Catalog information on the SNP and PubMed information on the research paper, respectively.

An example summary interface is shown in the following figure.

Upload a List of SNPs (Optional) ⑤
A group of SNPs of interest may be uploaded for visualization on the PleioNet program. To get started, click on the “Browse…” button. Select the desired SNP file (each SNP in a row) and upload. PleioNet will find all overlapping SNPs available in the GWAS catalog database and update the network display.

An example list of SNPs is shown in the following:

Download the example SNP ID file here (right click then download/save as). The example file was created on MacOS.

It is recommended that a relatively short list of SNPs is uploaded at a time in order for the most efficient upload wait time. Uploading larger lists will result in a longer network processing wait time.

Log Information ⑥
The log shows the number of SNPs, genes, and disease/traits that overlap with the users’ selections in the GWAS catalog database.

Export as png ⑦
Users can click on the “Export as png” button to save the network image. If you do not see this button, try to scroll down the page, or reduce the font size of your browsing window, or use a higher resolution monitor.

Additional Information
If you want to change the font size of the labels, you can click on the Settings in the menu bar and then adjust accordingly.

An example Font Size adjustment interface is shown in the following figure.

We tested our program using current versions of major web browsers, such as Safari, Chrome, Firefox, and Edge. Older versions of some web browsers may not support the network rendering step.

Because this program encompasses a broad array of information from the GWAS catalog, it can take time to render larger networks. Please be cautious when selecting how much information you choose to display and be patient when waiting for a new network to render.

PleioNet also works on mobile phone browsers. For example:

Summary Details

PleioNet: Where connections are revealed.

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PleioNet: Where connections are revealed.