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This article is part of the supplement: 22nd International Conference on Genome Informatics: Bioinformatics

Open Access Proceedings

Integrative analysis workflow for the structural and functional classification of C-type lectins

Geoffrey Koh1, Ariana Low1, Daren Poh1, Yujian Yao1, Say Kong Ng1, Victor Vai Tak Wong1, Vincent Vagenende1, Kong-Peng Lam1 and Dong-Yup Lee12*

Author affiliations

1 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore

2 Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117576, Singapore

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Citation and License

BMC Bioinformatics 2011, 12(Suppl 14):S5  doi:10.1186/1471-2105-12-S14-S5

Published: 14 December 2011

Abstract

Background

It is important to understand the roles of C-type lectins in the immune system due to their ubiquity and diverse range of functions in animal cells. It has been observed that currently confirmed C-type lectins share a highly conserved domain known as the C-type carbohydrate recognition domain (CRD). Using the sequence profile of the CRD, an increasing number of putative C-type lectins have been identified. Hence, it is highly needed to develop a systematic framework that enables us to elucidate their carbohydrate (glycan) recognition function, and discover their physiological and pathological roles.

Results

Presented herein is an integrated workflow for characterizing the sequence and structural features of novel C-type lectins. Our workflow utilizes web-based queries and available software suites to annotate features that can be found on the C-type lectin, given its amino acid sequence. At the same time, it incorporates modeling and analysis of glycans - a major class of ligands that interact with C-type lectins. Thereafter, the results are analyzed together with context-specific knowledge to filter off unlikely predictions. This allows researchers to design their subsequent experiments to confirm the functions of the C-type lectins in a systematic manner.

Conclusions

The efficacy and usefulness of our proposed immunoinformatics workflow was demonstrated by applying our integrated workflow to a novel C-type lectin -CLEC17A - and we report some of its possible functions that warrants further validation through wet-lab experiments.