irefindex_table: iRefIndex protein-protein interactions

In lagelab/Genoppi: genoppi

iRefIndex protein-protein interactions

Description

A dataset containing 396,984 published protein-protein interactions for 17,437 human genes in iRefIndex 17.0.

Usage

irefindex_table

Format

A data.frame with 396,984 rows and 5 variables:

Gene1

HGNC gene symbol of first protein

Gene2

HGNC gene symbol of second protein

Score.hpr.max

Highest PMID re-use

Score.lpr.max

Lowest PMID re-use

Score.np.max

Number of PMIDs

Details

This dataset was generated from the source BioPlex database by excluding all non-binary and non-human interactions. HGNC gene symbols were then extracted from the database along with the relevant score columns. Rows corresponding to the same gene pairs were merged into a single row by keeping the maximum scores.

Source

iRefIndex data (v17.0) downloaded on 2021-01-06 from: https://irefindex.vib.be/download/irefindex/data/archive/release_17.0/psi_mitab/MITAB2.6/

References

Razick S, Magklaras G, Donaldson IM. iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics. 2008;9:405. Published 2008 Sep 30. doi:10.1186/1471-2105-9-405

See Also

Other datasets: accession_gene_table, bioplex_table, example_data2, example_data3, example_data, genes_snps, gnomad_table, goa_bp_table, goa_cc_table, goa_mf_table, gtex_protein, gtex_rna, gwas_table, hgnc_group_table, hpa_rna, inweb_table, msigdb_c1_table, msigdb_c2_table, msigdb_c3_table, msigdb_c4_table, msigdb_c5_table, msigdb_c6_table, msigdb_c7_table, msigdb_h_table

lagelab/Genoppi documentation built on Oct. 13, 2022, 2:36 p.m.