Clustering of genes in prokaryotes was known for a long time. Their genes are grouped in operons, genes within operons share a common promoter unit. These genes are mostly functionally related. The genome of prokaryotes is relatively very simple and compact. In eukaryotes the genome is huge and only a small amount of it are functionally genes, furthermore the genes are not arranged in operons. Except for nematodes and trypanosomes; although their operons are different from the prokaryotic operons. In eukaryotes each gene has a transcription regulation site of its own. Therefore, genes don't have to be in close proximity to be co-expressed. Therefore, it was long assumed that eukaryotic genes were randomly distributed across the genome due to the high rate of chromosome rearrangements. But because the complete sequence of genomes became available it became possible to absolutely locate a gene and measure its distance to other genes.
The first eukaryote genome ever sequenced was that of Saccharomyces cerevisiae, or budding yeast, in 1996. Half a year after that Velculescu et al. (1997) published a research in which they had integrated SAGE data with the now available genome map. During a cell cycle different genes are active in a cell. Therefore, they used SAGE data from three moments of the cell cycle (log phase, S phase-arrested and G2/M-phase arrested cells). Because in yeast all genes have a promoter unit of their own it was not suspected that genes would cluster near to each other but they did. Clusters were present on all 16 yeast chromosomes.
A year later Cho et al. also reported (although in more detail) that certain genes are located near to each other in yeast.