Saving edge and node lists Pathway graph

If you are experienced in working with pathway plots and performing pathway analysis and wish to conduct an analysis not covered by Omics Studio, you have the option to export edges and nodes. This feature allows you to easily retrieve the pathway identified in Omics Studio.

💡 Give us feedback

If you frequently find yourself missing a specific function, we encourage you to contact the Omics Studio team and request its addition.

How to save edge or node list(s)

In the Pathway graph, you can click on the download button for either Save Edge List or Save Node List.

💡 Good to know

Please be aware that it only downloads a list of what is visible in the Pathway graph. Hence, if you filter and narrow down from 100 to 15 nodes, it will only download the list of the 15 nodes visible.

What is an Edge?

In pathway analysis, an edge represents a connection or relationship between two entities, known as nodes. Edges can signify various types of interactions depending on the context, such as physical interactions, regulatory relationships, or functional associations. In the context of Omics Studio, edges are often used to illustrate interactions between proteins or genes. Each edge is characterized by:

• From: Uniprot ID of the originating molecule.
• To: Uniprot ID of the target molecule.
• Type: The type of interaction, represented by different arrows in Omics Studio.

What is a Node?

A node in pathway analysis represents an individual entity within the pathway, such as a protein, gene, or molecule. Nodes are the fundamental units that are connected by edges to form a pathway. In Omics Studio, nodes are typically characterized by:

• Uniprot: Uniprot ID of the node.
• Pathway: Associated pathway.
• Label: Label of the node.
• fc: Fold change.
• logfc: Logarithm of the fold change.

This functionality allows you to effectively manage and analyze your pathway data outside of Omics Studio, enhancing your research capabilities.