Figure 1.

Combining sequence and expression data to make functional assignments. Each of five sets of orthologous genes is represented by a different shading, and each of four organisms is indicated by a different shape. Hence, genes with different shapes but the same shading are orthologs from different species. Edges (lines) in the networks represent co-expression between two genes. (a) The procedure used by Stuart et al. [9] to make functional annotations. Starting with genes from four organisms, they constructed 'metagenes', which are strict orthologous gene clusters. They then identified pairs of metagenes that are co-expressed in multiple organisms, leading to a metagene co-expression network. A set of metagenes that are densely connected to each other in the co-expression network are considered to share the same function. (b) The procedure used by Bergmann et al. [10] to identify functionally related genes across species. Starting from a set of co-expressed genes known to have the same function in organism a (S_a), the authors identify the set of sequence homologs in organism b (S_b') that are co-expressed. They then extend this co-expressed gene subset by including genes in organism b that show expression similarity but may not share sequence similarity (S_b'').