Gold_ReferenceSet {HPiP} | R Documentation

## Gold-standard Reference Set of Inter-Species PPIs

### Description

This dataset consists of experimentally validated human-SARS-CoV-2 interactions (positive set) and non-interacting pairs (negative set). The following data consists of:

- PPI: SARS-CoV-2-human protein-protein interactions (PPIs)

- Official Symbol Interactor A: SARS-CoV-2 gene names

- official Symbol Interactor B: human host gene names

- Pathogen_Protein: UniProt identifiers for SARS-CoV-2 virus

- Host_Protein: UniProt identifiers for human proteins

- class: labeled examples (both positive and negative)

### Usage

    data(Gold_ReferenceSet)

### Format

a data.frame containing 500 validated pairs (i.e., positive set) and 500 non-interacting pairs (i.e., negative set).

### Details

To construct this dataset, validated interactions (positive set) were retrieved from BioGrid database and were further filtered to only include those interactions provided by (Samavarchi-Tehrani et al., 2020). In this study, the authors mapped interaction between 27 SARS-CoV-2 and human proteins via the proximity-dependent biotinylation (BioID) approach. 500 SARS-CoV-2-host interaction pairs then randomly selected from all pairs to serve as positive examples. To construct negative examples,negative sampling were used using `get_negativePPI`.

### Source

https://www.biorxiv.org/content/10.1101/2020.09.03.282103v1

### References

Samavarchi-Tehrani,P. et al. (2020) A SARS-CoV-2-host proximity interactome. BioRxiv.

[Package HPiP version 1.0.0 Index]