Table 2. Results of test for feminization of X-linked transcripts in CDX males.

	Up-regulated in females		Down-regulated in females
	Up-regulated in CDX	Down-regulated in CDX	Up-regulated in CDX	Down-regulated in CDX
Observed	116.00	69.00	187.00	71.00
Expected	110.75	110.75	110.75	110.75

If CDX males (i.e. males with a paternally transmitted X-chromosome, produced by crossing a Control male to a DX female) have feminized X-chromosomes due to imprinting, then the change in expression of X-linked transcripts relative to Control males should be in the same direction as extant sexual dimorphism more often than expected by chance (first and last columns). Rather than being consistent with feminization, the data suggest increased expression of many X-linked transcripts in CDX males, regardless of whether these transcripts are usually male-biased or female-biased (first and third columns). This result is consistent with coevolution between the sex chromosomes (see main text). Note that the total number of transcripts in the analysis is less than the total number of X-linked genes because uninformative transcripts (i.e. those without gene annotation information, or those whose expression was the same across all samples) were filtered out during pre-processing.