Schema for Protein Interact. - Human Interacting Proteins from Gordon et al. (* = druggable)
  Database: wuhCor1    Primary Table: gordon2 Data last updated: 2020-04-29
Big Bed File: /gbdb/wuhCor1/bbi/gordon.bb
Item Count: 310
Format description: Browser extensible data, with extended fields for detail page
fieldexampledescription
chromNC_045512v2Reference sequence chromosome or scaffold
chromStart19620Start position in chromosome
chromEnd20658End position in chromosome
nameARF6Short Name of item
score988Score from 0-1000
strand++ or -
geneNamensp15SARS-Cov-2 gene name
UniProtP62330UniProt ID
drugDrug with effect on human gene
AppDrug Approval
descDescription
actActivity
pmidPMID
smilesSmiles
zincZINC ID

Sample Rows
 
chromchromStartchromEndnamescorestrandgeneNameUniProtdrugAppdescactpmidsmileszinc
NC_045512v21962020658ARF6988+nsp15P62330
NC_045512v21962020658RNF41994+nsp15Q9H4P4
NC_045512v21962020658NUTF2988+nsp15P61970
NC_045512v22160125381GOLGA7979+SpikeQ7Z5G4
NC_045512v22160125381ZDHHC5982+SpikeQ9C0B5
NC_045512v22539226217HMOX1994+orf3aP09601
NC_045512v22539226217TRIM59979+orf3aQ8IWR1
NC_045512v22539226217ARL6IP6865+orf3aQ8N6S5
NC_045512v22539226217VPS39879+orf3aQ96JC1
NC_045512v22539226217CLCC1921+orf3aQ96S66

Protein Interact. (gordon2) Track Description
 

Description

This track shows data from Gordon et al, 2020 "A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing".

The authors cloned, tagged, and expressed 26 of the mature proteins expressed by SARS-CoV-2 in 293 human cells and used affinity purification mass spectrometry (AP-MS) to identify human proteins that interact with viral proteins.

332 high confidence interactions are reported betwen human and viral proteins.

Display Conventions and Configuration

On the viral genome the coordinates of the viral protein are marked and labeled with the name of the human interactor.

The bed file also includes the MIST score * 1000. A MIST score of 1 is a highly reproducible and specific interaction, scores are multipled by 1000 for display purposes.

The set of interactions displayed here includes only the 332 "high confidence" interactions that met criteria for significance (using a MIST cutoff >= 0.7 as well as "a SAINTexpress BFDR <= 0.05 and an average spectral count >= 2.").

Methods

The tab delimited version of supplementary table 2 was downloaded from biorxiv. This table lists the viral protein that served as the "bait" and Uniprot identifiers of human proteins that were captured as "prey".

A version of the "UniProt Mature Protein Products (Polypeptide Chains)" track was then manually modified to rename ORFs to match paper nomenclature as indicated by Figure 1.

The table was then joined and MIST scores multipled by 1000 to produce a track reporting interactions.

References

Gordon et al, "A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing", Biorxiv 2020