Gold_ReferenceSet: Gold-standard Reference Set of Inter-Species PPIs

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

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.

mrbakhsh/HPiP documentation built on March 28, 2023, 4:35 p.m.