reactome: Reactome interactome

In fernandoPalluzzi/SEMdata: Datasets for SEM-based network analysis using the SEMgraph R package

Reactome interactome

Description

Interactome generated by merging Reactome pathways extracted using the graphite R package (update: April, 2020).

Usage

reactome

Format

"reactome" is an igraph network object of 9762 nodes and 416128 edges corresponding to the union of 1641 Reactome pathways.

Source

https://reactome.org

References

Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. PubMed PMID: 31691815. <doi:10.1093/nar/gkz1031>

Martini P, Sales G, Massa MS, Chiogna M, Romualdi C. Along signal paths: anempirical gene set approach exploiting pathway topology. Nucleic Acids Res. 41(1):e19. <https://doi.org/10.1093/nar/gks866>

Examples

summary(reactome)

# Reactome degrees of freedom
vcount(reactome)*(vcount(reactome) - 1)/2 - ecount(reactome)

# Reactome average shortest path length
mean_distance(reactome)

fernandoPalluzzi/SEMdata documentation built on June 27, 2022, 7:04 a.m.