For the comparison of S. cerevisiae and C. elegans data, conserved co-expressed gene pairs tend to code for members of the same protein complex [ 6] and such pairs show increased prediction accuracies for S. cerevisiae gene interactions [ 7].
The data of Conserved TFBS track, including associated TFs were downloaded from the UCSC Table Browser [ 26].
The stringency of our conditions may bias the data set toward conserved repeat elements.
On the other hand, GO terms related to ribosomal, cellular metabolic processes, and signal transduction were significantly overrepresented in the data set of conserved genes when compared with species-specific alleles (supplementary table S7, Supplementary Material online).
The deviation from the former study is likely due to the fact that they included only sequences present in all four conifer species used in their study thereby limiting severely the number of sequences (138) and likely enriching the data set for conserved sequences.
We then randomly assigned the values from the high, most conserved data set to the 1 2 orthologous pairs with the highest sequence identity, and the values from the low, less conserved data set to the 1 2 orthologous pairs with the lowest sequence identity, and counted the consistent cases.
In sorghum, gene pairs identified using the RAP annotation data were conserved significantly less frequently than the MSU rice gene pairs, whereas the fractions of rearranged pairs were significantly higher among all pair types in sorghum and Brachypodium, and among tandem gene pairs in maize.
Sequence alignment and secondary structure prediction of Nup188 from a broadly diverged range of species indicate that all Nup188 orthologs contain this SH3-like domain and that the position within the protein is conserved (data not shown).
As supported by the crystal structure data, these conserved residues are likely to be important for merlin function.
The IS system is an evolutionary wrapper system able to reduce the amount of data while conserving the largest amount of information available in the dataset.
