About species
For Species module, PCMD provides diverse pages and tools, such as Search species, Species-comparision, Species list.
By using Search species, users can access the metabolic characteristics of different species. We counted the predicted metabolites, experimentally measured metabolites and pairs of predicted protein-metabolites. Corresponding tables are provided for users to conveniently browse detailed information. Users can also explore plants with metabolites similar to their closest and farthest metabolites. To obtain detailed information about comparative analysis of metabolite similarity among different species, please refer to the Methods. Additionally, we categorized the predicted metabolites based on their uses, enabling the identification of the most enriched metabolites and the most enriched metabolite categories within each species. To access detailed information about the metabolite enrichment analysis, please refer to the Methods. Users can also query the predicted plant metabolic network and related literature of metabolite.
The ‘Species-comparision’ tool allows users to compare the specificity and commonness of metabolites between two different groups of plants at multiple taxonomic levels. When users choose a comparison by category, the PCMD provides three perspectives for comparison: taxonomy, seed and leaf characteristics, and reproductive characteristics. The results include information on common metabolites, specific metabolites unique to each group of plants, enrichment analysis of differential metabolites, and metabolite similarities between the two groups. Alternatively, users can upload two groups of plants as needed to compare differences in metabolites.
In the ‘Species list’ page, PCMD provides comprehensive information for 530 species, including predicted metabolite numbers, enzyme numbers, reactant numbers, and their respective rankings. Additionally, it offers an overview of species classification and metabolite numbers.
Species with both experimentally measured and predicted metabolites
| Species | Number of metabolites experimentally measured | Number of predicted metabolites supported by experiments |
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