All LocusLink genes from the tandem duplicate-free mouse genome were associated with the expression status (preferentially expressed, expressed, unknown).
It is known that enhancers in the human and mouse genomes are associated with active chromatin marks in a cell type specific manner, whereas promoter and insulator elements tend to be ubiquitously occupied in multiple cell lines (18).
However, a recent HapMap companion paper [ 9] reported that, although base-pairs in regions conserved between the human and mouse genomes were associated with low LD when sequence features were analyzed individually, the sequence conservation was not identified as an important predictor of LD in a multiple linear regression analysis.
All co-expression calculations were performed after eliminating 4547 Affymetrix probe sets (10% of those represented on the Affymetrix 430 2.0 Mouse Genome Array), which were associated with identifiers that included an "_s" or an "_x" suffix.
Numerous other gene families have been reported in the mouse genome that are also associated with reproduction such as the placentally expressed cathepsins [ 76- 78], Rhox transcription factors [ 79] and pregnancy-specific glycoproteins [ 80, 81], although their specific roles in reproduction remain largely unknown.
We also examined whether the differentially expressed genes in these pathways were associated with any of the mammary gland associated phenotypes found in the mouse genome informatics (MGI) database.
Initial comparisons of the human and mouse genome sequences revealed three classes of genes associated with divergent coding regions, those encoding extracellular, immune system, and reproductive proteins [ 20].
Of 1637 Known Genes, as shown in Figure 2, 41% were associated with bidirectional promoters in the mouse genome by the same gene name.
The phylostratigraphy-based analysis of trends associated with gene emergence in the mouse genome is well compatible with a frequent de novo emergence of orphan genes.
