InteRact

Analysis of affinity purification/tandem MS data with R

  • flexible : no strict input format
  • publication-ready figures

More info on the website

Install

The package is available from github:

devtools::install_github("VoisinneG/InteRact")

A shiny based GUI can be accessed here

Use

Load example protein group dataset and run InteRact:

data("proteinGroups_Cbl")
names(proteinGroups_Cbl)[1:10]
##  [1] "Protein.IDs"                   "Majority.protein.IDs"         
##  [3] "Peptide.counts..all."          "Peptide.counts..razor.unique."
##  [5] "Peptide.counts..unique."       "Protein.names"                
##  [7] "Gene.names"                    "Fasta.headers"                
##  [9] "Number.of.proteins"            "Peptides"
res <- InteRact(proteinGroups_Cbl, bait_gene_name = "Cbl")
## Contaminant proteins discarded
## Proteins with no gene name available discarded
## Number of theoretically observable peptides unavailable : used MW instead
## Merge protein groups associated to the same gene name (sum of intensities) 
## Rescale median intensity across conditions
## Replace missing values and perform interactome analysis for 1 replicates
## Nrep=1
## Averaging 1 interactomes

Identify specific interactors

res <- identify_interactors(res,
                            p_val_thresh = 0.001, 
                            fold_change_thresh = 3, 
                            n_success_min = 1, 
                            consecutive_success = TRUE)
print(res$interactor)
##  [1] "Cbl"      "Mccc1"    "Sh3kbp1"  "Ubash3a"  "Crkl"     "Pik3r1"  
##  [7] "Ywhah"    "Ywhag"    "Pik3ca"   "Grb2"     "StrepTag" "Pik3cd"  
## [13] "Emb"      "Pccb"     "Cox4i1"   "Myl6"     "Sod1"

Show summary table

sum_tbl <- summary_table(res)
head(sum_tbl[, c("bait", "names", "max_fold_change" ,"max_stoichio", "is_interactor")])
##   bait    names max_fold_change max_stoichio is_interactor
## 1  Cbl      Cbl      6028.12350    1.0000000             1
## 2  Cbl StrepTag       894.39480    1.8500618             1
## 3  Cbl     Pccb        22.03694    1.2265462             1
## 4  Cbl     Crkl       871.35901    0.6316826             1
## 5  Cbl    Ywhah       124.87974    0.2295337             1
## 6  Cbl    Ywhag       227.57076    0.2230696             1