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Open Access Database

Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank

Ryo Hashimoto12, Kazuko Hirose12, Taku Sato2, Nobuhiro Fukushima2, Nobuaki Miura3* and Shin-Ichiro Nishimura14*

Author Affiliations

1 Division of Advanced Chemical Biology, Graduate School of Life Science, Frontier Research Center for Post-Genomic Science and Technology, Hokkaido University, Sapporo 001-0021, Japan

2 Hokkaido STS, Inc., 5-1-16 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan

3 Sun Microsystems Laboratory for Computational Molecular Life Science, Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan

4 Drug-Seeds Discovery Research Laboratory, Hokkaido Center, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan

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BMC Systems Biology 2010, 4:91  doi:10.1186/1752-0509-4-91

Published: 29 June 2010

Abstract

Background

Glycans are involved in a wide range of biological process, and they play an essential role in functions such as cell differentiation, cell adhesion, pathogen-host recognition, toxin-receptor interactions, signal transduction, cancer metastasis, and immune responses. Elucidating pathways related to post-translational modifications (PTMs) such as glycosylation are of growing importance in post-genome science and technology. Graphical networks describing the relationships among glycan-related molecules, including genes, proteins, lipids and various biological events are considered extremely valuable and convenient tools for the systematic investigation of PTMs. However, there is no database which dynamically draws functional networks related to glycans.

Description

We have created a database called Glyco-Net http://www.glycoconjugate.jp/functions/ webcite, with many binary relationships among glycan-related molecules. Using search results, we can dynamically draw figures of the functional relationships among these components with nodes and arrows. A certain molecule or event corresponds to a node in the network figures, and the relationship between the molecule and the event are indicated by arrows. Since all components are treated equally, an arrow is also a node.

Conclusions

In this paper, we describe our new database, Glyco-Net, which is the first database to dynamically show networks of the functional profiles of glycan related molecules. The graphical networks will assist in the understanding of the role of the PTMs. In addition, since various kinds of bio-objects such as genes, proteins, and inhibitors are equally treated in Glyco-Net, we can obtain a large amount of information on the PTMs.