Extract Interactions using paxtoolsr from Pathway Commons

Question

[Norma]

I am looking for interactions between a protein (ACTB) and calcium and I want to use the paxtoolsr package. Is this possible? What code is necessary?

Answer 1

[cannin]

Here is code that would get you interactions that include actin or calcium from Pathway Commons:

library(paxtoolsr)

# READ AND FILTER PATHWAY COMMONS SIF INTERACTION TABLE ----
# With the file PathwayCommons12.reactome.hgnc.txt.gz downloaded from 
# https://www.pathwaycommons.org/archives/PC2/v12/ and uncompressed 
# NOTE: Either download directly or use downloadPc2() 

# Read file 
dat <- readSifnx("PathwayCommons12.reactome.hgnc.txt")

# Pathway Commons uses CHEBI identifiers for small molecules, chemicals, drugs, metabolites, etc. 
# IDs: 
# * Calcium: "CHEBI:29108" from https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29108
# * Actins from https://www.genenames.org/data/genegroup/#!/group/929

ca2 <- "CHEBI:29108"
actins <- c("ACTA1", "ACTA2", "ACTB", "ACTBL2", "ACTC1", "ACTG1", "ACTG2")

# Subset the SIF interaction table to those entries with either calcium or actin
# Use idsBothParticipants=TRUE if it must be both source and target nodes must come from ids parameter
sif <- filterSif(dat$edges, ids=c(ca2, actins), idsBothParticipants=FALSE)
sif_ids_both <- filterSif(dat$edges, ids=c(ca2, actins), idsBothParticipants=TRUE)

write.table(sif, "calcium_actin_interactions.txt", sep="\t", quote=FALSE, row.names=FALSE)

# > head(sif)
# # A tibble: 6 × 7
# PARTICIPANT_A INTERACTION_TYPE PARTICIPANT_B INTERACTION_DATA_SO… INTERACTION_PUB… PATHWAY_NAMES MEDIATOR_IDS
# <chr>         <chr>            <chr>         <chr>                <chr>            <chr>         <chr>       
# 1 ACTA2         in-complex-with  CALD1         Reactome             NA               Smooth Muscl… http://path…
# 2 ACTA2         in-complex-with  ITGA1         Reactome             NA               Smooth Muscl… http://path…
# 3 ACTA2         in-complex-with  ITGB5         Reactome             NA               Smooth Muscl… http://path…
# 4 ACTA2         in-complex-with  LMOD1         Reactome             NA               Smooth Muscl… http://path…
# 5 ACTA2         in-complex-with  MYH11         Reactome             NA               Smooth Muscl… http://path…
# 6 ACTA2         in-complex-with  MYL10         Reactome             NA               Smooth Muscl… http://path…