Table 1.

Overlapping genes in vertebrate genomes

	Number of genes analyzed	Number and fraction (in parentheses) of genes involved in overlaps	Chi-square test value (when compared to human)	Number of overlaps	Nested genes	Exon/exon overlaps (NATs) *		Intron/exon overlaps*
						Total	CDS involved
Human	22,291	2,978 (13.4)	NA	1,766	972	634	417	160
Chimpanzee	21,506	2,219 (10.3)	73.0888	1,276	665	479	317	132
Mouse	25,383	3,456 (13.6)	5.0750	2,053	1,071	819	565	163
Rat	22,159	1,080 (4.9)	895.1585	607	458	102	100	47
Chicken	17,709	1,960 (11.1)	32.2585	1,135	474	511	471	150
Fugu	20,796	993 (4.8)	880.5199	556	174	290	290	92
Zebrafish	23,524	1,625 (6.9)	472.4534	1,026	767	98	85	161

* excluding nested genes

Number of genes involved in overlaps is smaller than the number of overlaps multiplied by two since some genes are involved in more than one overlap. Multiple genes may be nested in one host gene as well as a gene may be overlapping other genes on both ends as reported previously [12]. Differences in overlapping genes frequencies between human and other species were tested using chi-square test. In all cases but mouse the chi-square is higher than critical value at α = 0.0005 and therefore differences are statistically significant. For mouse the difference is significant at α = 0.05. However, no definite conclusions can be drawn by this test results since some differences may result from the annotation problems but not real differences in the overlapping genes fraction.