Greenbaum D, Luscombe N M, Jansen R, Qian J, Gerstein M
Department of Genetics, Yale University, New Haven, Connecticut 06520-8114, USA.
Genome Res. 2001 Sep;11(9):1463-8. doi: 10.1101/gr.207401.
With the completion of genome sequences, the current challenge for biology is to determine the functions of all gene products and to understand how they contribute in making an organism viable. For the first time, biological systems can be viewed as being finite, with a limited set of molecular parts. However, the full range of biological processes controlled by these parts is extremely complex. Thus, a key approach in genomic research is to divide the cellular contents into distinct sub-populations, which are often given an "-omic" term. For example, the proteome is the full complement of proteins encoded by the genome, and the secretome is the part of it secreted from the cell. Carrying this further, we suggest the term "translatome" to describe the members of the proteome weighted by their abundance, and the "functome" to describe all the functions carried out by these. Once the individual sub-populations are defined and analyzed, we can then try to reconstruct the full organism by interrelating them, eventually allowing for a full and dynamic view of the cell. All this is, of course, made possible because of the increasing amount of large-scale data resulting from functional genomics experiments. However, there are still many difficulties resulting from the noisiness and complexity of the information. To some degree, these can be overcome through averaging with broad proteomic categories such as those implicit in functional and structural classifications. For illustration, we discuss one example in detail, interrelating transcript and cellular protein populations (transcriptome and translatome). Further information is available at http://bioinfo.mbb.yale.edu/what-is-it.
随着基因组序列测序的完成，生物学当前面临的挑战是确定所有基因产物的功能，并了解它们如何使生物体得以存活。生物学系统首次可以被视为有限的，由一组有限的分子部件组成。然而，由这些部件控制的所有生物过程的范围极其复杂。因此，基因组研究中的一个关键方法是将细胞内容物划分为不同的亚群，这些亚群通常被赋予一个“-组学”术语。例如，蛋白质组是基因组编码的所有蛋白质的完整集合，而分泌蛋白质组是从细胞中分泌出来的部分。进一步延伸，我们建议用“翻译组”来描述按丰度加权的蛋白质组成员，用“功能组”来描述由这些成员执行的所有功能。一旦定义并分析了各个亚群，我们就可以尝试通过将它们相互关联来重建整个生物体，最终实现对细胞的完整动态观察。当然，所有这些都是因为功能基因组学实验产生的大规模数据不断增加才成为可能。然而，信息的噪声和复杂性仍然带来许多困难。在某种程度上，可以通过与广泛的蛋白质组类别（如功能和结构分类中隐含的类别）进行平均来克服这些困难。为了说明这一点，我们详细讨论一个例子，即转录本和细胞蛋白质群体（转录组和翻译组）的相互关系。更多信息可在http://bioinfo.mbb.yale.edu/what-is-it获取。
