To further study the extent of gene expression conservation, we contrasted the mammalian conserved genes with the expression data from zebrafish.
These observations of expression divergence are not limited to the specific examples described above: all datasets have a fraction of divergently expressed genes despite the general trend of expression conservation observed over all data, underlining the importance of a dataset-specific measurement of expression conservation.
Notably, majority of the CNTs were widely expressed across developmental stages albeit exhibiting significantly lower expression, conservation and length compared to partially novel transcripts.
Our analysis shows that if the fraction of broadly expressed genes is large, the level of gene expression conservation is likely to be underestimated.
To estimate the expected values of co-module expression conservation (γ, equation 1) when the gene pairs show conserved expression patterns we used replicated experiments as two different data sets, both for mouse and human.
Note that there may be two steps in obtaining results of expression conservation of orthologs bioinformatically: the identification of orthologs and the measurement of expression conservation between orthologs.
Instead, we implemented a 'network-level' approach to estimate expression conservation (Figure 4).
This confirms that all the methods examined in this study are able to detect expression conservation.
In addition to expression conservation, expression divergence between species is also a measure for studying evolution of gene expression.
Because prior knowledge on the expression conservation for human-mouse orthologs is limited (expression conservation may not be associated with sequence conservation [5], [12], [13], [14], [15]), it is difficult to establish a benchmark for accurately evaluating the computational methods used for assessing expression conservation in terms of sensitivity and specificity.
Generally, the comparisons of EC distributions between human-mouse orthologs and random gene pairs by different methods all prove the theory of non-random expression conservation of orthologs.
