Implications

1. Peptides provide information on previously uncharacterized genes. By comparing protein sequences we can establish the relationships among gene family members or among closely related genes (Figure 3.9). Since proteins with similar sequences often have similar structures and hence functions, we can use this strategy to characterize new genes (Pearson 1996; Wood and Pearson 1999).

2. Functional elements can be found directly. Protein functional elements from databases such as PFAM, BLOCKS, and EC and many others can be searched directly. For example, it may be possible to find a functional element in common with co-expressed genes.

3. Enzyme Commission (EC) numbers classify enzymes based on the type of reaction catalyzed, substrate, and reagents/cofactors. Apart from the functional information, these numbers provide a controlled vocabulary to link the array information to other platforms and technologies. For example, EC numbers can be used to relate microarray results to data obtained from two-dimensional proteomic gels.

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