Peptide Information

Proteins are the functional manifestation of the genes represented on the array. When possible, the sequences of the proteins associated with the transcripts are provided in NetAffx™. Standard PFAM and BLOCKS motif annotations and BLASTp (Altschul et al. 1997) similarity searches are also included within NetAffx™. These standard-motif-based recognition systems annotate only approximately 51 % of the human proteome (Lander et al. 2001). To provide more extensive information the gen gene 2 9ene 3 gene 4

gene 2 9ene 3 gene 4

Fig. 3.9 Phylogenetic distances between genes having similar expression profiles. In this example, four transcripts with similar expression patterns were identified by clustering and examined for functional relationships. The protein sequences associated with the transcripts were aligned with ClustalX, and phylogenetic distances were measured with PHYLIP at (Retief 2000). Genes 2 and 3 are more closely related than genes 1 and 4. It is assumed that these distances reflect the similarities in protein function. Such an assumption can form the basis for further testing.

high-level Structural Classification of Proteins (SCOP) is included, which represents domains in the Protein Databank (PDB) based on a hierarchical structure of evolutionary relatedness (Murzin et al. 1995). The SCOP classifications are created at Affy-metrix and described in detail at whitepapers/scop_whitepaper.pdf. The goal is to provide protein family-level annotations that allow classification of probesets based on protein structure and function.

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