Functional Genomics

Having (almost) reached the end of Human Genome Project, the question that needs to be asked is: ``What next?''. The complete sequencing of the Human Genome is an immense task, which is now nearing completion. While much work remains to be done even there, there are a number of areas this knowledge opens up to research, which have thus far been nearly impossible to pursue. Among those are ``functional genomics'' - the search for understanding of the functionality of specific genes, their relations to diseases, their associated proteins and their participation in biological processes. Very little is known today. For example, in the plant Arabidopsis (whose sequencing has recently been completed), there is no functional knowledge for over 40% of the genes. Most of the knowledge gained so far in this area is the result of painstaking research of specific genes and proteins, based on complex biological experiments and homologies to known genes in other species. This ``Reductionist'' approach to functional genomics is hypothesis driven (i.e. it can be used to check an existing hypothesis, but not to suggest a new one). The advancements in both biological and computational techniques are now beginning to make possible a new approach: the ``Holistic'' research paradigm. This approach is based on high-throughput methods: global gene expression profiling (``transcriptome analysis'') and wide-scale protein profiling (``proteome analysis''). In the holistic approach, a researcher simultaneously measures a very large number of gene expression levels throughout a biological process, thereby obtaining insight into the functions and correlations between genes on a global level. Unlike the reductionist approach, these methods can generate hypotheses themselves.