More than a decade ago, a number of methods were proposed for the inference of 
protein interactions, using whole-genome information from gene clusters, gene 
fusions and phylogenetic profiles. This structural and evolutionary view of 
entire genomes has provided a valuable approach for the functional 
characterization of proteins, especially those without sequence similarity to 
proteins of known function. Furthermore, this view has raised the real 
possibility to detect functional associations of genes and their corresponding 
proteins for any entire genome sequence. Yet, despite these exciting 
developments, there have been relatively few cases of real use of these methods 
outside the computational biology field, as reflected from citation analysis. 
These methods have the potential to be used in high-throughput experimental 
settings in functional genomics and proteomics to validate results with very 
high accuracy and good coverage. In this critical survey, we provide a 
comprehensive overview of 30 most prominent examples of single pairwise protein 
interaction cases in small-scale studies, where protein interactions have either 
been detected by gene fusion or yielded additional, corroborating evidence from 
biochemical observations. Our conclusion is that with the derivation of a 
validated gold-standard corpus and better data integration with big experiments, 
gene fusion detection can truly become a valuable tool for large-scale 
experimental biology.