An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins.
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.
Yusufi
Faraaz Noor Khan
FN
Bioprocessing Technology Institute, Biomedical Sciences Institutes, Agency for Science, Technology and Research (A*STAR), Singapore.
Park
Wonjun
W
Lee
May May
MM
Lee
Dong-Yup
DY
D000117:Acetylglucosamine / Q000737:chemistry; D000465:Algorithms; D000818:Animals; D001709:Biotechnology / Q000379:methods*; D016466:CHO Cells; D019295:Computational Biology / Q000379:methods*; D006224:Cricetinae; D003412:Cricetulus; D005690:Galactose / Q000737:chemistry; D006023:Glycoproteins / Q000737:chemistry* / Q000378:metabolism; D006031:Glycosylation; D008358:Mannose / Q000737:chemistry; D019158:N-Acetylneuraminic Acid / Q000737:chemistry; D011134:Polysaccharides / Q000737:chemistry*; D012984:Software
D006023:Glycoproteins; D011134:Polysaccharides; D019158:N-Acetylneuraminic Acid; D008358:Mannose; D000117:Acetylglucosamine; D005690:Galactose