EUROCarbDB: An open-access platform for glycoinformatics

Glycobiology

Volumn 21, Issue 4, 2011, Pages 493-502

  Von Der Lieth, Claus Wilhelm ^a   Freire, Ana Ardá ^b   Blank, Dennis ^c   Campbell, Matthew P ^d,e,j   Ceroni, Alessio ^f   Damerell, David R ^f   Dell, Anne ^f   Dwek, Raymond A ^e   Ernst, Beat ^g   Fogh, Rasmus ^c,h   Frank, Martin ^a   Geyer, Hildegard ^c   Geyer, Rudolf ^c   Harrison, Mathew J ^h,k   Henrick, Kim ^h,l   Herget, Stefan ^a   Hull, William E ^a   Ionides, John ^h,l   Joshi, Hiren J ^a,h   Kamerling, Johannis P ^b   Leeflang, Bas R ^b   Lütteke, Thomas ^b,c   Lundborg, Magnus ⁱ   Maass, Kai ^c   Merry, Anthony ^h   Ranzinger, René ^a,m   Rosen, Jimmy ^b   Royle, Louise ^d,e   Rudd, Pauline M ^d,e   Schloissnig, Siegfried ^a   Stenutz, Roland ⁱ   Vranken, Wim F ^h   Widmalm, Göran ⁱ   Haslam, Stuart M ^f,g   more..

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b UTRECHT UNIVERSITY   (Netherlands)

^c JUSTUS LIEBIG UNIVERSITY   (Germany)

^d UNIVERSITY COLLEGE DUBLIN   (Ireland)

^e UNIVERSITY OF OXFORD   (United Kingdom)

^f IMPERIAL COLLEGE LONDON   (United Kingdom)

^g UNIVERSITY OF BASEL   (Switzerland)

^h EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

ⁱ STOCKHOLM UNIVERSITY   (Sweden)

^j MACQUARIE UNIVERSITY   (Australia)

^k ROYAL PRINCE ALFRED HOSPITAL   (Australia)

^l WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^m UNIVERSITY OF GEORGIA   (United States)

more..

Author keywords

databases; glycoinformatics; informatics tools; open source

Indexed keywords

CARBOHYDRATE; GLYCAN;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DATA BASE; EUROCARBDB DATABASE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL;

ANIMALS; CARBOHYDRATE CONFORMATION; CARBOHYDRATES; COMPUTATIONAL BIOLOGY; DATABASES AS TOPIC; GLYCOMICS; HUMANS; MODELS, MOLECULAR; MOLECULAR WEIGHT; ONLINE SYSTEMS; SOFTWARE;

EID: 79952549595     PISSN: 09596658     EISSN: 14602423     Source Type: Journal    
DOI: 10.1093/glycob/cwq188     Document Type: Article

References (59)

1. Abd Hamid UM, Royle L, Saldova R, Radcliffe CM, Harvey DJ, Storr SJ, Pardo M, Antrobus R, Chapman CJ, Zitzmann N, et al. 2008. A strategy to reveal potential glycan markers from serum glycoproteins associated with breast cancer progression. Glycobiology. 18:1105-1118. (Pubitemid 352762845)
2. An HJ, Kronewitter SR, de Leoz ML, Lebrilla CB. 2009. Glycomics and disease markers. Curr Opin Chem Biol. 13:601-607.
3. Aoki-Kinoshita KF. 2008. An introduction to bioinformatics for glycomics research. PLoS Comput Biol. 4:e1000075.
4. Aoki KF, Yamaguchi A, Ueda N, Akutsu T, Mamitsuka H, Goto S, Kanehisa M. 2004. KCaM (KEGG Carbohydrate Matcher): A software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. 32: W267-W272. (Pubitemid 38997342)
5. Arnold JN, Saldova R, Hamid UM, Rudd PM. 2008. Evaluation of the serum N-linked glycome for the diagnosis of cancer and chronic inflammation. Proteomics. 8:3284-3293.
6. Babu P, North SJ, Jang-Lee J, Chalabi S, Mackerness K, Stowell SR, Cummings RD, Rankin S, Dell A, Haslam SM. 2009. Structural characterisation of neutrophil glycans by ultra sensitive mass spectrometric glyco-mics methodology. Glycoconj J. 26:975-986.
7. Bielik AM, Zaia J. 2009. Historical overview of glycoanalysis. Methods Mol Biol. 600:9-30.
8. Bleckmann C, Geyer H, Lieberoth A, Splittstoesser F, Liu Y, Feizi T, Schachner M, Kleene R, Reinhold V, Geyer R. 2009. O-glycosylation pattern of CD24 from mouse brain. Biol Chem. 390:627-645.
9. Bleckmann C, Geyer H, Reinhold V, Lieberoth A, Schachner M, Kleene R, Geyer R. 2009. Glycomic analysis of N-linked carbohydrate epitopes from CD24 of mouse brain. J Proteome Res. 8:567-582.
10. Blow N. 2009. Glycobiology: A spoonful of sugar. Nature. 457:617-620.
11. Bohne-Lang A, Lang E, Forster T, von der Lieth CW. 2001. LINUCS: Linear notation for unique description of carbohydrate sequences. Carbohydr Res. 336:1-11. (Pubitemid 32995898)
12. Campbell MP, Royle L, Radcliffe CM, Dwek RA, Rudd PM. 2008. GlycoBase and autoGU: Tools for HPLC-based glycan analysis. Bioinformatics. 24:1214-1216. (Pubitemid 351594175)
13. Ceroni A, Dell A, Haslam SM. 2007. The GlycanBuilder: A fast, intuitive and flexible software tool for building and displaying glycan structures. Source Code Biol Med. 7:2-3.
14. Ceroni A, Maass K, Geyer H, Geyer R, Dell A, Haslam SM. 2008. GlycoWorkbench: A tool for the computer-assisted annotation of mass spectra of glycans. J Proteome Res. 7:1650-1659.
15. Cooper CA, Harrison MJ, Wilkins MR, Packer NH. 2001. GlycoSuiteDB: A new curated relational database of glycoprotein glycan structures and their biological sources. Nucleic Acids Res. 29:332-335. (Pubitemid 32054485)
16. Cooper CA, Joshi HJ, Harrison MJ, Wilkins MR, Packer NH. 2003. GlycoSuiteDB: A curated relational database of glycoprotein glycan structures and their biological sources. 2003 update. Nucleic Acids Res. 31:511-513. (Pubitemid 36150442)
17. Dennis JW, Lau KS, Demetriou M, Nabi IR. 2009. Adaptive regulation at the cell surface by N-glycosylation. Traffic. 10:1569-1578.
18. Doubet S, Albersheim P. 1992. CarbBank. Glycobiology. 2:505.
19. Doubet S, Bock K, Smith D, Darvill A, Albersheim P. 1989. The Complex Carbohydrate Structure Database. Trends Biochem Sci. 14:475-477. (Pubitemid 19284340)
20. Frank M, Schloissnig S. 2010. Bioinformatics and molecular modeling in glycobiology. Cell Mol Life Sci. 67:2749-2772.
21. Harvey DJ. 1999. Matrix-assisted laser desorption/ionization mass spec-trometry of carbohydrates. Mass Spectrom Rev. 18:349-450.
22. Harvey DJ. 2006. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update covering the period 1999-2000. Mass Spectrom Rev. 25:595-662. (Pubitemid 44018026)
23. Harvey DJ. 2008. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update covering the period 2001-2002. Mass Spectrom Rev. 27:125-201. (Pubitemid 351315898)
24. Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M. 2006. KEGG as a glycome informatics resource. Glycobiology. 16:63R-70R.
25. Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, et al. 2008. Remediation of the protein data bank archive. Nucleic Acids Res. 36: D426-D433. (Pubitemid 351149761)
26. Herget S, Ranzinger R, Maass K, von der Lieth CW. 2008. GlycoCT-a unifying sequence format for carbohydrates. Carbohydr Res. 232:2162-2171.
27. Jansson PE, Stenutz R, Widmalm G. 2006. Sequence determination of oligo-saccharides and regular polysaccharides using NMR spectroscopy and a novel web-based version of the computer program CASPER. Carbohydr Res. 341:1003-1010.
28. Kikuchi N, Kameyama A, Nakaya S, Ito H, Sato T, Shikanai T, Takahashi Y, Narimatsu H. 2005. The carbohydrate sequence markup language (CabosML): An XML description of carbohydrate structures. Bioinformatics. 21:1717-1718. (Pubitemid 40542741)
29. Lehr T, Geyer H, Maass K, Doenhoff MJ, Geyer R. 2007. Structural characterization of N-glycans from the freshwater snail Biomphalaria glabrata cross-reacting with Schistosoma mansoni glycoconjugates. Glycobiology. 17:82-103. (Pubitemid 44932817)
30. Liu L, Telford JE, Knezevic A, Rudd PM. 2010. High-throughput glycoanaly-tical technology for systems glycobiology. Biochem Soc Trans. 38:1374-1377.
31. Lowe HJ, Barnett GO. 1994. Understanding and using the medical subject headings (MeSH) vocabulary to perform literature searches. JAMA. 271:1103-1108. (Pubitemid 24106508)
32. Lütteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth CW. 2006. GLYCOSCIENCES.de: An Internet portal to support glycomics and glycobiology research. Glycobiology. 16:71R-81R.
33. Maass K, Ranzinger R, Geyer H, von der Lieth CW, Geyer R. 2007. Glyco-Peakfinder - de novo composition analysis of glycoconjugates. Proteomics. 7:4435-4444.
34. Marino K, Bones J, Kattla JJ, Rudd PM. 2010. A systematic approach to protein glycosylation analysis: A path through the maze. Nat Chem Biol. 6:713-723.
35. Marth JD, Grewal PK. 2008. Mammalian glycosylation in immunity. Nat Rev Immunol. 8:874-887.
36. Morelle W, Michalski JC. 2007. Analysis of protein glycosylation by mass spectrometry. Nat Protoc. 2:1585-1602. (Pubitemid 47028845)
37. North SJ, Hitchen PG, Haslam SM, Dell A. 2009. Mass spectrometry in the analysis of N-linked and O-linked glycans. Curr Opin Struct Biol. 19:498-506.
38. Packer NH, von der Lieth CW, Aoki-Kinoshita KF, Lebrilla CB, Paulson JC, Raman R, Rudd P, Sasisekharan R, Taniguchi N, York WS. 2008. Frontiers in glycomics: Bioinformatics and biomarkers in disease. An NIH white paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11-13, 2006). Proteomics. 8:8-20.
39. Pang PC, Tissot B, Drobnis EZ, Morris HR, Dell A, Clark GF. 2009. Analysis of the human seminal plasma glycome reveals the presence of immunomodulatory carbohydrate functional groups. J Proteome Res. 8:4906-4915.
40. Raman R, Venkataraman M, Ramakrishnan S, Lang W, Raguram S, Sasisekharan R. 2006. Advancing glycomics: Implementation strategies at the consortium for functional glycomics. Glycobiology. 16:82R-90R.
41. Ranzinger R, Frank M, von der Lieth CW, Herget S. 2009. Glycome-DB.org: A portal for querying across the digital world of carbohydrate sequences. Glycobiology. 19:1563-1567.
42. Ranzinger R, Herget S, Wetter T, Von Der Lieth CW. 2008. GlycomeDB - integration of open-access carbohydrate structure databases. BMC Bioinformatics. 9:384.
43. Royle L, Campbell MP, Radcliffe CM, White DM, Harvey DJ, Abrahams JL, Kim YG, Henry GW, Shadick NA, Weinblatt ME, et al. 2008. HPLC-based analysis of serum N-glycans on a 96-well plate platform with dedicated database software. Anal Biochem. 376:1-12.
44. Rudd PM, Elliott T, Cresswell P, Wilson IA, Dwek RA. 2001. Glycosylation and the immune system. Science. 291:2370-2376. (Pubitemid 32231792)
45. Saldova R, Royle L, Radcliffe CM, Abd Hamid UM, Evans R, Arnold JN, Banks RE, Hutson R, Harvey DJ, Antrobus R, et al. 2007. Ovarian cancer is associated with changes in glycosylation in both acute-phase proteins and IgG. Glycobiology. 17:1344-1356. (Pubitemid 350131311)
46. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, et al. 2009. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 37:D5-15.
47. Stenutz R. 2009. Automatic spectrum interpretation based on increment rules. In von der Lieth CW, Lütteke T, et al., editors. Bioinformatics for Glycobiology and Glycomics: An Introduction. Wiley-Blackwell. p. 311-320.
48. Taniguchi N, Hancock W, Lubman DM, Rudd PM. 2009. The second golden age of glycomics: From functional glycomics to clinical applications. J Proteome Res. 8:425-426.
49. Tharmalingam T, Marino K, Rudd PM. 2010. Platform technology to identify potential disease markers and establish heritability and environmental determinants of the human serum N-glycome. Carbohydr Res. 345:1280-1282.
50. Tissot B, Ceroni A, Powell AK, Morris HR, Yates EA, Turnbull JE, Gallagher JT, Dell A, Haslam SM. 2008. Software tool for the structural determination of glycosaminoglycans by mass spectrometry. Anal Chem.
51. Toukach FV, Knirel YA. 2005. New database of bacterial carbohydrate structures. Proceeding of the XVIII International Symposium on Glycoconjugates, 216-217.
52. Vanderschaeghe D, Festjens N, Delanghe J, Callewaert N. 2010. Glycome profiling using modern glycomics technology: Technical aspects and applications. Biol Chem. 391:149-161.
53. Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, et al. 2010. PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 38:D308-D317.
54. Von Der Lieth CW, Bohne-Lang A, Lohmann KK, Frank M. 2004. Bioinformatics for glycomics: Status, methods, requirements and perspectives. Brief Bioinform. 5:164-178.
55. Von Der Lieth CW, Lütteke T, Frank M. 2006. The role of informatics in glycobiology research with special emphasis on automatic interpretation of MS spectra. Biochim Biophys Acta. 1760:568-577.
56. Von Witzendorff D, Maass K, Pich A, Ebeling S, Kolle S, Kochel C, Ekhlasi-Hundrieser M, Geyer H, Geyer R, Topfer-Petersen E. 2009. Characterization of the acidic N-linked glycans of the zona pellucida of prepuberal pigs by a mass spectrometric approach. Carbohydr Res. 344:1541-1549.
57. Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas P, Ulrich EL, Markley JL, Ionides J, Laue ED. 2005. The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins. 59:687-696. (Pubitemid 40695845)
58. Widmalm G. 2007. General NMR spectroscopy of carbohydrates and confor-mational analysis in solution. In Kamerling JP, editor. Comprehensive Glycoscience. Oxford: Elsevier, p. 101-132.
59. Zaia J. 2008. Mass spectrometry and the emerging field of glycomics. Chem Biol. 15:881-892.