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. 2019 Jan 8;47(D1):D1118-D1127.
doi: 10.1093/nar/gky965.

CMAUP: a database of collective molecular activities of useful plants

Xian Zeng  1   2 , Peng Zhang  2 , Yali Wang  2 , Chu Qin  2 , Shangying Chen  2 , Weidong He  2 , Lin Tao  2   3 , Ying Tan  1 , Dan Gao  1 , Bohua Wang  4   5 , Zhe Chen  3 , Weiping Chen  4 , Yu Yang Jiang  1 , Yu Zong Chen  2
Affiliations

CMAUP: a database of collective molecular activities of useful plants

Xian Zeng et al. Nucleic Acids Res. .

Abstract

The beneficial effects of functionally useful plants (e.g. medicinal and food plants) arise from the multi-target activities of multiple ingredients of these plants. The knowledge of the collective molecular activities of these plants facilitates mechanistic studies and expanded applications. A number of databases provide information about the effects and targets of various plants and ingredients. More comprehensive information is needed for broader classes of plants and for the landscapes of individual plant's multiple targets, collective activities and regulated biological pathways, processes and diseases. We therefore developed a new database, Collective Molecular Activities of Useful Plants (CMAUP), to provide the collective landscapes of multiple targets (ChEMBL target classes) and activity levels (in 2D target-ingredient heatmap), and regulated gene ontologies (GO categories), biological pathways (KEGG categories) and diseases (ICD blocks) for 5645 plants (2567 medicinal, 170 food, 1567 edible, 3 agricultural and 119 garden plants) collected from or traditionally used in 153 countries and regions. These landscapes were derived from 47 645 plant ingredients active against 646 targets in 234 KEGG pathways associated with 2473 gene ontologies and 656 diseases. CMAUP (http://bidd2.nus.edu.sg/CMAUP/) is freely accessible and searchable by keywords, plant usage classes, species families, targets, KEGG pathways, gene ontologies, diseases (ICD code) and geographical locations.

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Figures

Figure 1.
Figure 1.
The homepage of CMAUP web interface. The webpage allows users to search plants by keywords (e.g. plant name, target, disease, pathway), search plants by ingredients, browse plants by plant usage classes and other options, and access plants by the interactive world map.
Figure 2.
Figure 2.
Ingredients of a specific plant. (A) Chemical ingredients are shown in the graphs based on distributions of few important physiochemical properties (e.g. molecular weight, XlogP, number of hydrogen bond donor). (B) Chemical structure images are provided when available. The chemical information, reference of plant-ingredient association and distribution of the ingredient across plants can be accessed by click the ‘SEE DETAILS’ button (C).
Figure 3.
Figure 3.
An example webpage of protein targets of a specific plant. Target proteins are categorized into classes based on ChEMBL target classification. External links are provided in the table in the right pane.
Figure 4.
Figure 4.
Activity landscape of a specific plant. The interactive heatmap allows users to access the detailed information of activity by clicking the individual cells.
Figure 5.
Figure 5.
KEGG pathways of a specific plant. The pie chart shows the distribution of pathways in each KEGG Orthology category. The bar chart presents the top 10 enriched pathways ordered by the adjusted P-values. The bottom table lists detailed information of enriched KEGG pathways.
Figure 6.
Figure 6.
Gene Ontology terms of a specific plant. Distributions of GO terms in biological process, molecular function and cellular component categories are displayed in the top pie charts. The bottom table lists detailed information about enriched GO terms.
Figure 7.
Figure 7.
Human diseases related to a specific plant. The upper pie chart shows the number of diseases in each WHO ICD-10 disease category. The below table lists detailed information about these diseases.
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