This view first displays interactions, as defined by gene interaction data derived from Pathway Commons. Interactions in this view have been limited to those between members of a pathway, and to three interaction types: "controls state change," "controls expression," and "interacts."

The presence of variants in the interacting genes can be indicated in this view.

If a subset of interacting genes are selected, pathway names and a count of their gene members can be displayed, as well as a heatmap of expression.

Global filters affect this view. Any sample-based filters set here and/or variant filters set here determine what variants appear in this view. If no global filters are set, all are shown.

In the "String view" plot, genes are sorted into groups: those that control other genes, those that are both controlled by and control other genes, and those that are controlled by other genes. These three groups are arranged on axes from left to right, with the direction of control pointing right.

On the middle axis, interaction lines end in arrows to indicate direction of control.

Interactions are color-coded by type.

A black circle underneath the gene name indicates the presence of variants when "Show variants" is checked.

Each type of interaction can be shown/hidden with the checkboxes in the string plot.

Variants in a gene can be shown/hidden with the "Show variants" checkbox.

Clicking on a gene name will hide interactions not involving that gene.

Click "Show all interactions" to restore hidden interactions.

Selected genes
This view supports the creation of a set of selected genes, and you can select a gene in three ways: 1) Clicking on its gene name in the string plot, 2) Selecting it from the drop-down menu under the string plot, or 3) Clicking "Select all." Selected genes appear below the string plot.

Clicking on a gene name in the selected genes list will display a set of links for that gene: View gene model, View interactions, View chronology, and Go to GeneCards.

Genes can be removed from the selected genes list by clicking the "x" after their names, or you may remove all of them by clicking "Clear list."

When a set of genes (or a single gene) has been selected, a heatmap of RNA-Seq expression will also be generated below the string plot.

Clicking the "Create gene set" button will take you to the gene set page, which will be populated with the list of currently selected genes.

Pathways
Every time a gene is added to or removed from the selected genes list, Vizome checks to see if any pathways contain all of the selected genes. If so, a list of those pathways will appear on the top right.

Clicking on the small green arrow at the end of the pathway name will export a list of that pathway's gene members with a count of samples with variants per gene.

Clicking on the pathway name itself will open a pathway view in a new window.