Workflow for the reconstruction of the immunome interactome. The general steps taken to reconstruct the immunome interactome are shown. The cylinders represent data repositories from which data was retrieved. Parallelograms represent data, either retrieved from databases or obtained by analyses. Rectangles represent performed analyses. T cell microarray experiments available in ArrayExpress and the GEO databases were retrieved. These experiments included at least 3 samples. The selected experiments were normalized using the R/Bioconductor libraries. Batch effect analysis was done and all experiments were merged or integrated. Jackknife Pearson correlation coefficient was calculated for the integrated dataset. Immunome proteins were retrieved from the Immunome knowledge Base (IKB) and the KEGG pathways databases. Major immune response pathways from the KEGG were used to supplement the IKB immunome proteins. Immunome interactome was obtained by retrieving PPIs for the immunome protein dataset from the iRefIndex database. To reduce noisy PPIs we used the ppiTrim method and further filtered its output of redundant and non-immune response PPIs. The Jackknife correlation coefficients were used as link weights.