Cited by 175Glycosylation and Glycoproteins ResearchMachine Learning in Bioinformaticsvaccines and immunoinformatics approaches

NetCGlyc 1.0: Prediction of mammalian C-mannosylation sites

Julenius, Karin·2007·Glycobiology

Abstract

C-mannosylation is the attachment of an alpha-mannopyranose to a tryptophan via a C-C linkage. The sequence WXXW, in which the first Trp becomes mannosylated, has been suggested as a consensus motif for the modification, but only two-thirds of known sites follow this rule. We have gathered a data set of 69 experimentally verified C-mannosylation sites from the literature. We analyzed these for sequence context and found that apart from Trp in position +3, Cys is accepted in the same position. We also find a clear preference in position +1, where a small and/or polar residue (Ser, Ala, Gly, and Thr) is preferred and a Phe or a Leu residue discriminated against. The Protein Data Bank was searched for structural information, and five structures of C-mannosylated proteins were obtained. We showed that modified tryptophan residues are at least partly solvent exposed. A method predicting the location of C-mannosylation sites in proteins was developed using a neural network approach. The best overall network used a 21-residue sequence input window and information on the presence/absence of the WXXW motif. NetCGlyc 1.0 correctly predicts 93% of both positive and negative C-mannosylation sites. This is a significant improvement over the WXXW consensus motif itself, which only identifies 67% of positive sites. NetCGlyc 1.0 is available at http://www.cbs.dtu.dk/services/NetCGlyc/. Using NetCGlyc 1.0, we scanned the human genome and found 2573 exported or transmembrane transcripts with at least one predicted C-mannosylation site.

Integrity signals

Registry

Crossref · 10.1093/glycob/cwm050

Cites

50 of 50 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Julenius, K.
Affiliations
Stockholm University (SE)
Corresponding author
Julenius, Karin
Venue
Glycobiology
Published
2007-05-09
Volume
17
Issue
8
Pages
868-876
ISSN
  • 0959-6658 (ISSN-L)
  • 1460-2423
OpenAlex
W2152890174
Cited by
174
References
50
Citations by year
2026: 5 · 2025: 7 · 2024: 11 · 2023: 3 · 2022: 8 · 2021: 11 · 2020: 15 · 2019: 8 · 2018: 11 · 2017: 15 · 2016: 15 · 2015: 6 · 2014: 14 · 2013: 8 · 2012: 9
FWCI
2.65
Type
journal article
Language
en
Open access
closed
Locations
  • Glycobiology (publishedVersion)
  • PubMed (publishedVersion)
Funders
Knut och Alice Wallenbergs Stiftelse
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Glycosylation and Glycoproteins Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Keywords
C-mannosylation, glycosylation site prediction, sequence context, solvent exposure, neural network classifier, mammalian proteins, human genome, transmembrane proteins
MeSH terms
Algorithms, Amino Acid Sequence, Animals, Glycoproteins, Humans, Mammals, Mannose, Models, Molecular, Molecular Sequence Data, Genome, Human, Neural Networks, Computer, Amino Acid Motifs, Databases, Protein

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review