Biological space gene function

The dimensionality of chemical structure space exceeds that of known biological functional space. The dimensionality of biological functional space has increased in recent years due to the discovery of a multitude of genes, largely from the Human Genome Project. This chapter, however, will focus on chemical diversity rather than functional diversity. Quantification of chemical diversity involves two areas first, the predefmition of a chemical space, accomplished by selection of a diversity metric and a compound representation (i.e., molecular descriptors) and second, a rational subset selection, or classification, method dependent on efficient dimensionality reduction. Here, we describe these methods, prerequisites for a definition... 

Unlike genes, which are physically located at a locus on a chromosome based on their linkage to other sequences of DNA (although they may move owing to transpositions and recombination events), small molecules that induce phenotypic variation in biological systems are themselves not physically located in a space. Thus, if small molecules are to be mapped to a common space, then the space must be considered to represent abstract space in the sense that it is mathematically derived [74-76], This abstract space, which we will refer to as chemical space , is formed by multiple dimensions, or axes, such that the relative distance between small molecules represented by points becomes a measure of their structural or functional similarity. The notion is that certain regions in this space correspond to small molecules that have similar structure or function. 

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