string-protein-interaction-analysis-with-omicverse

STRING protein interaction analysis with omicverse

Overview

Invoke this skill when the user has a list of genes and wants to explore STRING protein–protein interactions via omicverse. The

workflow mirrors [t_network.ipynb](../../omicverse_guide/docs/Tutorials-bulk/t_network.ipynb), covering species selection, S

TRING API queries, and quick visualisation of the resulting network.

Instructions

1. Set up libraries

• Import omicverse as ov and call ov.utils.ov_plot_set() (or ov.plot_set()) to match omicverse aesthetics.

1. Collect gene inputs

• Accept a curated list of gene symbols (gene_list = [...]).
• Encourage the user to flag priority genes or categories so you can colour-code groups in the plot.

1. Assign metadata for plotting

• Build dictionaries mapping genes to types and colours, e.g. `gene_type_dict = dict(zip(gene_list, ['Type1']5 + ['Type2']6

)) and gene_color_dict = {...}`.

• Remind users that consistent group labels improve legend readability.

1. Query STRING interactions

• Call ov.bulk.string_interaction(gene_list, species_id) where species_id is the NCBI taxonomy ID (e.g. 4932 for yeast).
• Inspect the resulting DataFrame for combined scores and evidence channels to verify coverage.

1. Construct the network object

• Initialise ppi = ov.bulk.pyPPI(gene=gene_list, gene_type_dict=..., gene_color_dict=..., species=species_id).
• Run ppi.interaction_analysis() to fetch and cache STRING edges.

1. Visualise the network

• Generate a default plot with ppi.plot_network() to reproduce the notebook figure.
• Mention that advanced styling (layout, node size, legends) can be tuned through ov.utils.plot_network keyword arguments if

the user requests adjustments.

1. Troubleshooting

• Ensure gene symbols match the species—STRING expects case-sensitive identifiers; suggest mapping Ensembl IDs to symbols when

queries fail.

• If the API rate-limits, instruct the user to wait or provide a cached interaction table.
• For missing interactions, recommend enabling STRING's "add_nodes" option via ppi.interaction_analysis(add_nodes=...) to exp

and the network.

Examples

• "Retrieve STRING interactions for FAA4 and plot the network highlighting two gene classes."
• "Download the STRING edge table for my Saccharomyces cerevisiae gene panel and colour nodes by module."
• "Extend the network by adding the top five predicted partners before plotting."

References

• Tutorial notebook: [t_network.ipynb](../../omicverse_guide/docs/Tutorials-bulk/t_network.ipynb)
• STRING background: string-db.org
• Quick copy/paste commands: [reference.md](reference.md)