Omics Data in TCM
High-throughput data can be used to provide a comprehensive inventory of all the biological processes of cells, display their complexity and increase data accuracy.18 An accurate picture of the differential expression of experimental samples is important for defining precise targets and networks.18 An increasing number of “-omics” methods, such as genomics, transcrip- tomics, proteomics and metabonomics, are gradually being adopted by TCM researchers.16 Integrating various omics data and analyzing the data using bioinformatics will assist in establishing new TCM databases, which will facilitate searching prescriptions, herbs, ingredients, targets, drugs and diseases described above, as well as for elucidating the molecular mechanism of TCM, discovery of novel ingredients in TCM and combination therapy (Figure 10.6). Here, I review the data resources from omics studies.
Genomics in TCM
With rapid advances in high-throughput sequencing technologies and greatly reduced costs, a new discipline called “herbal genomics” or TCM genomics has emerged.19,2° Researchers are now systematically categorizing medicinal herbs by sequencing, assembling, and annotating their
Figure 10.6 The benefits to TCM of integrating various omics data and analyzing the data by bioinformatics.
genomes, and by analyzing their genes’ functions.19 Among these, Gano- derma lucidum (ChiZhi) is one of the best known medical macrofungi. G. lucidum is more than just an ordinary fungus; it has long been used in traditional Chinese medicinal remedies and for the promotion of health and longevity in many Asian countries.21’22 The G. lucidum resource includes genome assembly, 16 113 gene models and their corresponding gene function annotations, and transcriptomic data from three different developmental stages, namely, mycelia, primordial, and fruiting bodies.23 It also presents predicted gene clusters and chemical compounds identified in G.
The purpose of TCM genomics is to study the genome of prescriptions and to discover the molecular mechanism of TCM acting on the human genome. It prescriptions precise and simple, and pushes TCM to the molecular level or finds the gene for active ingredients.20 One TCM genomics database, the Medicinal Plant Metabolomics Resource, includes 14 taxonomically diverse medicinal plant species. This information is summarized in Table 10.3. The database contains not only the genome information of 14 taxonomically diverse medicinal plant species, but also transcriptome and metabolome data. Users can download the data directly from the website (http://met- netweb.gdcb.iastate.edu/mpmr_public/).