Human genome annotation

Most recently, in silico methods have been apphed to the systems biology of metabolic pathways. An analysis of the human genome assigns 2709 human enzymes to 896 bioreactions 622 of the enzymes are assigned roles in 135 predicted metabolic pathways. The predicted pathways closely match the known nutritional requirements of humans. This analysis identifies probable omissions in the human genome annotation in the form of 203 pathway holes (missing enzymes within the predicted pathways). The predicted human metabolic map is described by a Pathway/Genome Database called HumanCyc, which is available at http //HumanCyc.org/. 

Finally attention should be called to the most comprehensive and current treatment of the human genome and its impact in science and medicine, which was the subject of an entire special issue of Science. (The issue contained an interesting 4 Vi x 6 foot chart of the annotation of the Celera human genome assembly [33].)... 

Shoemaker DD et al. Experimental annotation of the human genome using... 

Probes can be antibodies, other binding proteins constructed from protein fusions, or even oligonucleotide aptamers. While completion of the Human Genome Project has enabled access to content for nuclide acid arrays, the content for protein arrays is largely based upon available antibody libraries. Thus, the commercialization of protein microarrays remains largely dependent upon both commercial and institutional providers of protein content. These providers must also permit access to the data-based protein annotations. These are necessary in order for the protein array to be useful as a bioinformatics tool. 

The current situation in bioinformatics is characterized by an avalanche of DNA sequences from the human genome project and similar programs and, consequently, an exponential increase in DNA sequences but only a linear increase in protein 3D structures. While multitudes of putative genes have been annotated, up to 90% of all known DNA sequences have no assigned, i.e., experimentally proven, function. From this situation arise the need for interpretation of DNA sequences by information technology, and moreover, analysis of functional genomics and proteomics (see Chapter 15). 

Bailey, L. C., Jr., Searls, D. B. Overton, G. C. (1998). Analysis of EST-driven gene annotation in human genomic sequence. Genome Res 8,362-76. 

The strategy employed is to fractionate cells into organelles and examine the proteins in each organelle. This approach provides smaller mixtures of proteins to be examined, with the prospect of analyzing more proteins overall, allows observations to be correlated within the frame of reference of organelle biology, and occasionally allows the contribution of new observations about which proteins occur in which part of the cell, that is, annotation of the human genome. 

The completion of the human genome with high-quality annotation revealed approximately 30,000 genes,2 3 and with it, much exuberance about the... 

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