Although the Human Genome Project (and the various plant & animal genome projects that preceded it and continue on) was often hyped as the key to unlocking human biology, it's only the first step in a bigger process. Genes code for proteins. Of far greater utility than a genome map -- and of far greater complexity -- is a map of protein interaction, sometimes called a "proteome." Proteins form the building blocks of tissues, and their interactions are the basis for biological systems. In short, proteins actually carry out the details of being a living being.
A draft map has just been completed of the protein interactions for Drosophila melanogaster, the fruit fly. The abstract is available here; the full article PDF is here. According to the researchers (at CuraGen and a variety of universities), the "map serves as a starting point for a systems biology modeling of multicellular organisms including humans." They also state in their report that they intend for the map "to serve as a public resource for interested scientists."
Believers in the precautionary principle and the application of responsibility and foresight to biotech research should be really pleased by this. Protein interaction maps are critical for understanding the more subtle results of genetic manipulation. Among the concerns reasonable people have about bioengineering is the possibility of unforeseen interactions between apparently distinct biological systems. As biologists build more of these proteomic maps, the better ability we'll have to avoid problems down the road -- and a better idea we'll have about how to fix things to survive in a rapidly changing climate.
Proteins are not the only things that genes code for... as far as I know, organisms also create carbohydrates and other chemcials and structures (e.g. bones).. These don't just appear by magic, they are a "second-order" result of the genes that code for the proteins and structures that then produce these other chemicals and structures.
The GM laws in many countries are completely protein oriented, and say that if there is no GM-modified protein detectable in the food, then all is fine. Pity if the gene codes for changes in the organism & those changes result in new non-protein chemicals with unknown properties and effects.