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Pharmacogenomics |
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Susumu Goto
Associate Professor, Bioinformatics Center, Institute for Chemical Research, Kyoto University |
Database of Chemical Compounds and Glycans for Pharmacogenomics
We are developing a database
of chemical structures with the information on reactions and pathways, which
allows us genome-scale analysis such as expression data analysis. In this study,
we mainly focus on the carbohydrate structure database GLYCAN and develop glycan
related technologies for the pharmacogenomics applications.
1. Carbohydrate structure database: GLYCAN
GLYCAN is a database of carbohydrate structures collected from research articles. The main portion of GLYCAN came from CarbBank, which is the most famous carbohydrate database but has been unfortunately discontinued due to the lack of funding. We reorganized the structures into newly developed KCF (KEGG Chemical Function) format, which is more suitable for structure-based applications, e.g. inputting new data and searching similar structures.
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2. Composite structure map: CSM
Composite structure map is a map illustrating all possible variations of carbohydrate
structures within organisms, where the edges and nodes represent glycosyltrasferases
and carbohydrate structures (Figure). It is constructed as a bridge between
carbohydrate functions and structures, and is able to display, for example,
expression data of glycosyltransferases in a compact manner.
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3. Carbohydrate structure input tool: KegDraw
KegDraw is an intuitive drawing tool for carbohydrate structures. KegDraw is
a Java application, so it runs on locally in a platform-independent manner
and it allows the drawing of not only glycan structures but also atomic coordination
of chemical compounds. Glycan structures drawn in KegDraw can be used as queries
to search against GLYCAN and other databases by KCaM structure search server
and as inputs for the database updates.
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