Fig. 5.

The “Complex” annotated protein interaction map. Known complexes from the Munich Information Center for Protein Sequences (MIPS) database and their biological relations were apparent in the reconstructed protein-protein interaction network derived from the high-confidence AP/MS data set. We colored components in a same MIPS complex the same, with gray nodes representing unannotated proteins. This reconstructed network captured a global organization of protein complexes, in particular for protein assemblies related to RNA synthesis, chromatin remodeling, DNA replication and repair, protein synthesis, and protein and RNA degradation (proteasome and exosome). Proteins in transport complexes were connected among themselves, but the proteins that they transport were not captured in this mapping. Some labels have been removed for clarity, and the complete annotations are provided in the Supplementary Material.