Using our methodology, we were able to identify differences between the sporulation processes of the two species,
despite conserved functions, revealing the plasticity of the functional modules. Comparing genomic properties of different
organisms is of fundamental importance and several examples, which exhibit characteristic situations and illustrate the
potential of combining sequence and expression data to address particular evolutionary issues, are presented in :
- Supplementary Note S8 : Conservation of expression between organisms can be used for improving functional gene annotation.
- Supplementary Note S9 : Co-expression can be used for refining orthologous links between organisms.
The availability of data for numerous species allows knowledge about the biological role of shared proteins to be
transferred from one organism to another one. There are numerous "model" organisms that are well studied and can be used
for inferring the function of ORFs newly sequenced. As an illustration, we can consider the S. cerevisiae gene ATG8
(YBL078C) and its S. pombe ortholog SPBP8B7.24C. After the superimposition procedure, ATG8 (YBL078C) exhibited a low Ei
value and a low Delta-i value (
Figure 5A). Similarity between their expression profiles was
expected and visually verified (
Figure 5B, 1). In this case, sequence homology and expression
profiles during sporulation are conserved between the two yeasts. The SGD database (Christie, Weng et al. 2004) contains
experimental data and a precise description of the gene ATG8 (Lang, Schaeffeler et al. 1998). It encodes a protein that
mediate attachment of autophagosomes to microtubules. In the GeneDB database (Hertz-Fowler, Peacock et al. 2004) the only
information about the gene SPBP8B7.24C (a "predicted autophagy related microtubule-associated protein") is inferred from
homology. Indeed, functions are often assigned to ORFs newly sequenced on the basis of sequence homology with a known
protein. Despite the success of this approach, the absence of a direct relationship between the sequence similarity and
functional similarity of two proteins is a well-recognized limitation. However, the demonstration of conservation of
expression substantially strengthens the functional gene annotation. The evolutionary conservation of expression patterns
between species provides functional information, complementary to that from sequence data, and helps identify genes that
are genuinely functionally related. Our analysis offer a rigorous approach to associate these two sets of data.
