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An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins

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Abstract

Advances in high-throughput techniques have led to the creation of increasing amounts of glycome data. The storage and analysis of this data would benefit greatly from a compact notation for describing glycan structures that can be easily stored and interpreted by computers. Towards this end, we propose a fixed-length alpha-numeric code for representing N-linked glycan structures commonly found in secreted glycoproteins from mammalian cell cultures. This code, GlycoDigit, employs a pre-assigned alpha-numeric index to represent the monosaccharides attached in different branches to the core glycan structure. The present branch-centric representation allows us to visualize the structure while the numerical nature of the code makes it machine readable. In addition, a difference operator can be defined to quantitatively differentiate between glycan structures for further analysis. The usefulness and applicability of GlycoDigit were demonstrated by constructing and visualizing an N-linked glycosylation network.

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Abbreviations

CHO:

Chinese Hamster ovary

Gal:

Galactose

GlcNAc:

N-Acetylglucosamine

IUPAC:

International Union for Pure and Applied Chemistry

Man:

Mannose

NeuNAc:

N-Acetylneuraminic acid

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Acknowledgments

This work was supported by the Biomedical Research Council of A*STAR (Agency for Science, Technology and Research), Singapore. The authors would like to thank Dr. Niki Wong and Mr. Robin J. Philp for their valuable comments and suggestions.

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Authors and Affiliations

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

    Faraaz Noor Khan Yusufi, Wonjun Park, May May Lee & Dong-Yup Lee

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

    Dong-Yup Lee

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  1. Faraaz Noor Khan Yusufi
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  2. Wonjun Park
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  3. May May Lee
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  4. Dong-Yup Lee
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Correspondence to Dong-Yup Lee.

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Yusufi, F.N.K., Park, W., Lee, M.M. et al. An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins. Bioprocess Biosyst Eng 32, 97–107 (2009). https://doi.org/10.1007/s00449-008-0226-4

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  • DOI: https://doi.org/10.1007/s00449-008-0226-4

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