testDomainAssociation: PFAM domain-domain association analysis

In ccb-hms/BioPlexAnalysis: Applications and downstream analysis of BioPlex PPI data

PFAM domain-domain association analysis

Description

Identifies statistically associated protein domain pairs connected by a disproportionally high number of protein-protein interactions.

Usage

testDomainAssociation(gr)

Arguments

gr	An object of class graph storing the BioPlex PPIs. Typically obtained via bioplex2graph.

Details

Given PFAM domain annotations for each node of the graph, the function assesses domain pairs connected by two or more interactions for significance using Fisher’s exact test based on 1) the number of interactions connecting both domains; 2) the numbers of interactions involving either domain individually; and 3) the number of interactions not involving either domain.

It is important to note that although the domain association analysis identifies pairs of PFAM domains whose parent proteins interact preferentially across the network, this does not necessarily mean that these domains themselves are responsible for the interaction. Many may simply be passengers that associate as a consequence of interactions mediated by contacts elsewhere in the protein sequence.

Value

A data.frame containing all tested PFAM domain pairs ordered by association strength.

References

Huttlin et al. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell, 184(11):3022-3040.e28, 2021.

Examples

  # (1) obtain BioPlex PPI network for 293T cells
  library(BioPlex)
  df <- getBioPlex(cell.line = "HCT116", version = "1.0")
  hct.gr <- bioplex2graph(df)
 
  # (2) annotate PFAM domains
  library(AnnotationHub)
  ah <- AnnotationHub()
  orgdb <- query(ah, c("orgDb", "Homo sapiens"))
  orgdb <- orgdb[[1]]
  hct.gr <- annotatePFAM(hct.gr, orgdb)

  # (3) domain-domain association analysis
  res <- testDomainAssociation(hct.gr)

ccb-hms/BioPlexAnalysis documentation built on Jan. 29, 2023, 6:55 p.m.