Search for new nodes Pathway graph

Searching for new nodes allows you to discover interactions between your nodes (e.g., transcriptomics) of interest. Whether you are looking for upstream or downstream interactions, the Search for new nodes tool provides the functionality you need.

This tool uses the Reactome.org database to find interactions and can be used to identify connections between nodes and pathways. The search can be performed as either a lookup or using a shortest path algorithm, depending on the chosen search criteria. You can also apply the Directed edges only or Ignore metabolites criteria if needed.

Available searches

• Find upstream When selecting the Find upstream function, Omics Studio uses the Reactome.org database to find nodes (e.g., proteomics) that interact with the selected nodes upstream.

• Find downstream When selecting the Find downstream function, Omics Studio uses the Reactome.org database to find nodes (e.g., transcriptomics) that interact with the selected nodes downstream.

• Shortest path (internal) When selecting the Shortest path (internal) function, Omics Studio uses the Reactome.org database to find the shortest connection route between the selected nodes (e.g., proteomics) within the already selected pathways. This means the result will be limited to the ability to connect the targets within the chosen pathways.

• Shortest path (external) When selecting the Shortest path (external) function, Omics Studio uses the Reactome.org database to find the shortest connection route between the selected nodes (e.g., transcriptomics) without any pathway limitations.

Available search criteria

• Directed edges only If this criterion is enabled, the searches will only consider interactions downstream from the first selected node to the second selected node (A -> interactor(s) -> B). If this criterion is disabled, Omics Studio will try all possible connections, e.g.:

  • A -> interactor(s) -> B,
  • A <- interactor(s) -> B,
  • A -> interactor(s) <- B, and
  • A <- interactor(s) <- B)

• Ignore Metabolites If this criterion is enabled, the searches will only consider nodes as connections. This is recommended as some metabolites are involved in numerous interactions. If this criterion is disabled, all metabolites will also be considered.

By utilizing these search functions and criteria, you can effectively expand your pathway analysis and uncover new interactions relevant to your research.