Skip to contents

Get Protein-Protein Interaction Enrichment

Source: R/stringdb.R
rba_string_enrichment_ppi.Rd

Even when there is no annotation for your input proteins, STRING can Compare your Given proteins interactions pattern with the background proteome-wide interaction distribution to determine if your given set of proteins are functionally related.

Usage

rba_string_enrichment_ppi(
  ids,
  species = NULL,
  required_score = NULL,
  background = NULL,
  ...
)

Arguments

ids

Your protein ID(s). It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information.

species

Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606. (Recommended, but optional if your input is less than 100 IDs.)

required_score

Numeric: A minimum of interaction score for an interaction to be included in the image. if not supplied, the threshold will be applied by STRING Based in the network. (low Confidence = 150, Medium Confidence = 400, High Confidence = 700, Highest confidence = 900)

background

character vector: A set of STRING protein IDs to be used as the background proteome. Only STRING IDs are acceptable. (See rba_string_map_ids to map your IDs.)

...

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

Value

A list with protein-protein interaction enrichment results.

Corresponding API Resources

"POST https://string-db.org/api/[output_format]/ppi_enrichment?identifiers= [your_identifiers]&[optional_parameters]"

References

  • Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D605–D612, https://doi.org/10.1093/nar/gkaa1074

  • STRING API Documentation

  • Citations note on STRING website

See also

rba_string_map_ids

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_homology_inter(), rba_string_homology_intra(), rba_string_interaction_partners(), rba_string_interactions_network(), rba_string_map_ids(), rba_string_network_image(), rba_string_version()

Examples

# \donttest{
rba_string_enrichment_ppi(ids = c("p53", "BRCA1", "cdk2", "Q99835",
       "CDC42", "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1"),
    species = 9606)
# }