Literature DB >> 23325765

Using databases and web resources for glycomics research.

Kiyoko F Aoki-Kinoshita1.   

Abstract

Many databases of carbohydrate structures and related information can be found on the World Wide Web. This review covers the major carbohydrate databases that have potential utility for glycoscientists and researchers entering the glycosciences. The first half provides a brief overview of carbohydrate databases and web resources (including a history of carbohydrate databases and carbohydrate notations used in these databases), and the second half provides a guide that can be used as an index to determine which resources provide the data of most interest to the user.

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Year:  2013        PMID: 23325765      PMCID: PMC3617328          DOI: 10.1074/mcp.R112.026252

Source DB:  PubMed          Journal:  Mol Cell Proteomics        ISSN: 1535-9476            Impact factor:   5.911


  38 in total

Review 1.  GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research.

Authors:  Thomas Lütteke; Andreas Bohne-Lang; Alexander Loss; Thomas Goetz; Martin Frank; Claus-W von der Lieth
Journal:  Glycobiology       Date:  2005-10-20       Impact factor: 4.313

Review 2.  Advancing glycomics: implementation strategies at the consortium for functional glycomics.

Authors:  Rahul Raman; Maha Venkataraman; Subu Ramakrishnan; Wei Lang; S Raguram; Ram Sasisekharan
Journal:  Glycobiology       Date:  2006-02-14       Impact factor: 4.313

3.  A global representation of the carbohydrate structures: a tool for the analysis of glycan.

Authors:  Kosuke Hashimoto; Shin Kawano; Susumu Goto; Kiyoko F Aoki-Kinoshita; Masayuki Kawashima; Minoru Kanehisa
Journal:  Genome Inform       Date:  2005

4.  UniCarb-DB: a database resource for glycomic discovery.

Authors:  Catherine A Hayes; Niclas G Karlsson; Weston B Struwe; Frederique Lisacek; Pauline M Rudd; Nicolle H Packer; Matthew P Campbell
Journal:  Bioinformatics       Date:  2011-03-12       Impact factor: 6.937

5.  Large-scale identification of N-glycosylated proteins of mouse tissues and construction of a glycoprotein database, GlycoProtDB.

Authors:  Hiroyuki Kaji; Toshihide Shikanai; Akiko Sasaki-Sawa; Hongling Wen; Mika Fujita; Yoshinori Suzuki; Daisuke Sugahara; Hiromichi Sawaki; Yoshio Yamauchi; Takashi Shinkawa; Masato Taoka; Nobuhiro Takahashi; Toshiaki Isobe; Hisashi Narimatsu
Journal:  J Proteome Res       Date:  2012-08-13       Impact factor: 4.466

6.  A strategy for identification of oligosaccharide structures using observational multistage mass spectral library.

Authors:  Akihiko Kameyama; Norihiro Kikuchi; Shuuichi Nakaya; Hiromi Ito; Takashi Sato; Toshihide Shikanai; Yoriko Takahashi; Katsutoshi Takahashi; Hisashi Narimatsu
Journal:  Anal Chem       Date:  2005-08-01       Impact factor: 6.986

7.  Printed covalent glycan array for ligand profiling of diverse glycan binding proteins.

Authors:  Ola Blixt; Steve Head; Tony Mondala; Christopher Scanlan; Margaret E Huflejt; Richard Alvarez; Marian C Bryan; Fabio Fazio; Daniel Calarese; James Stevens; Nahid Razi; David J Stevens; John J Skehel; Irma van Die; Dennis R Burton; Ian A Wilson; Richard Cummings; Nicolai Bovin; Chi-Huey Wong; James C Paulson
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-24       Impact factor: 11.205

8.  Frontal affinity chromatography: sugar-protein interactions.

Authors:  Hiroaki Tateno; Sachiko Nakamura-Tsuruta; Jun Hirabayashi
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

9.  KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.

Authors:  Kiyoko F Aoki; Atsuko Yamaguchi; Nobuhisa Ueda; Tatsuya Akutsu; Hiroshi Mamitsuka; Susumu Goto; Minoru Kanehisa
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

10.  GlycomeDB--a unified database for carbohydrate structures.

Authors:  René Ranzinger; Stephan Herget; Claus-Wilhelm von der Lieth; Martin Frank
Journal:  Nucleic Acids Res       Date:  2010-11-02       Impact factor: 16.971

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  12 in total

Review 1.  Integration of systems glycobiology with bioinformatics toolboxes, glycoinformatics resources, and glycoproteomics data.

Authors:  Gang Liu; Sriram Neelamegham
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2015-04-13

Review 2.  Humanizing glycosylation pathways in eukaryotic expression systems.

Authors:  Amjad Hayat Khan; Hadi Bayat; Masoumeh Rajabibazl; Suriana Sabri; Azam Rahimpour
Journal:  World J Microbiol Biotechnol       Date:  2016-11-11       Impact factor: 3.312

Review 3.  Carbohydrates in Cyberspace.

Authors:  Elizabeth Yuriev; Paul A Ramsland
Journal:  Front Immunol       Date:  2015-06-10       Impact factor: 7.561

4.  Introducing glycomics data into the Semantic Web.

Authors:  Kiyoko F Aoki-Kinoshita; Jerven Bolleman; Matthew P Campbell; Shin Kawano; Jin-Dong Kim; Thomas Lütteke; Masaaki Matsubara; Shujiro Okuda; Rene Ranzinger; Hiromichi Sawaki; Toshihide Shikanai; Daisuke Shinmachi; Yoshinori Suzuki; Philip Toukach; Issaku Yamada; Nicolle H Packer; Hisashi Narimatsu
Journal:  J Biomed Semantics       Date:  2013-11-26

Review 5.  Biological roles of glycans.

Authors:  Ajit Varki
Journal:  Glycobiology       Date:  2016-08-24       Impact factor: 4.313

Review 6.  A Golden Age for Working with Public Proteomics Data.

Authors:  Lennart Martens; Juan Antonio Vizcaíno
Journal:  Trends Biochem Sci       Date:  2017-01-22       Impact factor: 13.807

Review 7.  The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human.

Authors:  Anthony P Corfield
Journal:  Microorganisms       Date:  2018-08-02

8.  LM-GlycomeAtlas Ver. 1.0: A Novel Visualization Tool for Lectin Microarray-Based Glycomic Profiles of Mouse Tissue Sections.

Authors:  Chiaki Nagai-Okatani; Kiyoko F Aoki-Kinoshita; Shuichi Kakuda; Misugi Nagai; Kozue Hagiwara; Katsue Kiyohara; Noriaki Fujita; Yoshinori Suzuki; Takashi Sato; Kiyohiko Angata; Atsushi Kuno
Journal:  Molecules       Date:  2019-08-15       Impact factor: 4.411

9.  Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts.

Authors:  Philip V Toukach; Ksenia S Egorova
Journal:  Nucleic Acids Res       Date:  2015-08-18       Impact factor: 16.971

10.  Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update).

Authors:  Michael Böhm; Andreas Bohne-Lang; Martin Frank; Alexander Loss; Miguel A Rojas-Macias; Thomas Lütteke
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

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