Table 1

A few representative studies on overlapping genes, organized alphabetically with summary of principle conclusions and data type
Authors
 Year
 Genomes
 IE
 VE
 SM
 Genes & Homology
 Evolutionary Process
Lillo & Krakauer
 2007
 58 Prokaryote
 RC & TC
 MA & MB
 NS
 Study of E. coli genome
 Neutrality & Selection
Boi et al [2]
 2004
 ? Eukaryote
 GR
 NS
 NS
 NS
 Selection on regulation
Das & Yanofsky [3]
 1989
 1 Prokaryote
 TC
 NS
 NS
 Study of 2 genes
 Selection on expression
Fukuda et al. [6]
 1999
 2 Prokaryote
 NS
 NS
 NE
 Study of 480 & 677 genes
 Neutral mutation to stop codon
Fukuda et al [7]
 2003
 3 Prokaryote
 NS
 NS
 NS
 NS
 Neutral mutation to stop and start
Johnson & Chisholm [13]
 2004
 198 Prokaryote
 TC
 NS
 NS
 Study of 2 genomes
 Selection on expression
Krakauer [15]
 2000
 NS
 RC & TC
 MA
 NS
 NS
 Selection on replication and expression
Krakauer [16]
 2002
 NS
 RC & TC
 MA & MB
 NS
 NS
 Selection on replication and expression
Makalowska et al. [22]
 2005
 7 Eukaryote
 GR
 NS
 NS
 NS
 Neutrality
Merino et al. [25]
 1994
 28 Prok & 8 Euk
 GR
 NS
 NS
 Study of E. coli genome
 Selection on regulation
Miyata & Yasunaga [24]
 1978
 1 Prokaryote
 NS
 MA
 NS
 Study of -x174
 Selection on replication
Normark et al. [26]
 1983
 ? Prokaryote
 TC
 NS
 NS
 NS
 Selection on expression
Oppenheim & Yanofsky [28]
 1980
 1 Prokaryote
 TC
 NS
 NS
 E. coli Trp operon
 Selection on expression
Pavesi et al. [29]
 1997
 ? Viral
 NS
 MB
 IC
 NS
 Selection on coding
Rogozin et al. [30]
 2002
 ? Prokaryotes
 NS
 MB
 NS
 NS
 Selection on coding
Sakharkar et al [31]
 2005
 9 Prokaryotes
 RC
 NS
 NS
 Study of 2 genomes
 Selection on replication
Sander & Schulz [32]
 1979
 2 Prokaryote
 NS
 MB
 NS
 Study of SV40 & -x174 genes
 Selection on coding
Welch et al. [39]
 2000
 1 Prokaryote
 TC
 NS
 NS
 Study of V anguillarum
 Selection for iron biosynthesis

Key: IE – Immediate Effect, VE – variational effect, SM – Statistical Model NS – Not in Study, TC – translational coupling, RC – replicative compression, GR antisense gene regulation MB – mutational buffering, MA – mutational amplification, NE – Neutral expectation under statistical model, IC – Shannon information content of overlap. The ? symbols records an unknown number lineages. The column labeled "Genes and detailed homology" captures the pattern of many studies to couple the statistics of large databases with the detailed analysis of a small number of overlapping genes from well studied genomes. The difference between selection on expression versus selection on regulation seeks to discriminate between co-expression (as in a codon) and active inhibition or activation (such as through anti-sense), The difference between selection on replication and selection on coding reflects a difference only in emphasis as both imply a greater number of genes in a shorter sequence.

Lillo and Krakauer Biology Direct 2007 2:22   doi:10.1186/1745-6150-2-22

Open Data