Get STRING Network Interactions

This function retrieves STRING interaction pairs among the input proteins, including the combined score and separate scores for each evidence channel. You can expand the network using the add_nodes parameter.

Usage

rba_string_interactions_network(
  ids,
  species = NULL,
  required_score = NULL,
  add_nodes = NULL,
  network_type = "functional",
  use_query_labels = FALSE,
  network_term_id = NULL,
  ...
)

Arguments

ids

Your protein IDs. It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information.
Alternatively, you can retrieve interactions among proteins annotated with a STRING functional term by setting ids = NULL and supplying network_term_id.

species

Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606. Required when using network_term_id; otherwise recommended, but required if your input contains more than 10 unique IDs.

required_score

Numeric (between 0 and 1000): Minimum interaction score required for an interaction to be included in the returned network. If omitted, STRING applies a network-dependent threshold. Common confidence thresholds are 150 (low), 400 (medium), 700 (high), and 900 (highest).

add_nodes

Numeric: Number of neighboring proteins to add to the network. For identifier-based requests, if omitted, STRING determines the value from the number of input IDs:

1. One ID: STRING adds 10 proteins to retrieve its interaction neighborhood.

2. Multiple IDs: STRING adds no proteins, so only interactions among the input proteins are returned.

network_type

Character: One of:

• "functional": (default) Edges indicate both physical and functional associations.

• "physical": Edges indicate that two proteins have a physical interaction or are parts of a complex.

use_query_labels

Logical: (default = FALSE) Use the names supplied in ids as node labels instead of STRING's default labels.

network_term_id

Character: A functional term identifier (e.g. a Gene Ontology, KEGG, or Reactome identifier). Instead of using proteins supplied through ids, STRING constructs the network from proteins annotated with the specified term. Set ids = NULL and supply species.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A data frame in which each row is a network interaction and the columns contain interactor information and interaction scores:

• stringId_A: STRING identifier (protein A)

• stringId_B: STRING identifier (protein B)

• preferredName_A: common protein name (protein A)

• preferredName_B: common protein name (protein B)

• ncbiTaxonId: NCBI taxon identifier

• score: combined score

• nscore: gene neighborhood score

• fscore: gene fusion score

• pscore: phylogenetic profile score

• ascore: co-expression score

• escore: experimental score

• dscore: database score

• tscore: textmining score

Details

This function returns interactions among the supplied proteins and any neighboring proteins added through add_nodes. To retrieve interactions between your input proteins and all their STRING interaction partners, see rba_string_interaction_partners.

Corresponding API Resources

"POST https://string-db.org/api/{output-format}/network?identifiers= {your_identifiers}&{optional_parameters}"
"POST https://string-db.org/api/{output-format}/network?network_term_id= {your_term}&{optional_parameters}"

References

• Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Katerina Nastou, Farrokh Mehryary, Radja Hachilif, Annika L Gable, Tao Fang, Nadezhda T Doncheva, Sampo Pyysalo, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D638–D646, https://doi.org/10.1093/nar/gkac1000

• STRING API Documentation

• Citations note on STRING website

See also

rba_string_map_ids, rba_string_interaction_partners, rba_string_network_image, rba_string_enrichment_ppi

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_image(), rba_string_enrichment_ppi(), rba_string_functional_terms(), rba_string_homology_inter(), rba_string_homology_intra(), rba_string_interaction_partners(), rba_string_map_ids(), rba_string_network_image(), rba_string_version()

Examples

# \donttest{
rba_string_interactions_network(ids = c("9606.ENSP00000269305",
    "9606.ENSP00000398698",
    "9606.ENSP00000275493"),
    network_type = "functional")
# }
# \donttest{
rba_string_interactions_network(ids = c("9606.ENSP00000269305",
    "9606.ENSP00000398698",
    "9606.ENSP00000275493"),
    species = 9606,
    add_nodes = 10)
# }
# \donttest{
rba_string_interactions_network(
    ids = NULL,
    network_term_id = "GO:0050852",
    species = 9606,
    required_score = 900
)
# }