Determining Lectin Specificity from Glycan Array Data Using Motif Segregation and GlycoSearch Software

Doron Kletter1, Zheng Cao2, Marshall Bern1, Brian Haab2

1 Palo Alto Research Center, Palo Alto, California, 2 Van Andel Research Institute, Grand Rapids, Michigan
Publication Name:  Current Protocols in Chemical Biology
Unit Number:   
DOI:  10.1002/9780470559277.ch130028
Online Posting Date:  June, 2013
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Abstract

The glycan array is a powerful tool for investigating the specificities of glycan‐binding proteins. By incubating a glycan‐binding protein on a glycan array, the relative binding to hundreds of different oligosaccharides can be quantified in parallel. Based on these data, much information can be obtained about the preference of a glycan‐binding protein for specific subcomponents of oligosaccharides, or motifs. In many cases, the analysis and interpretation of glycan array data can be time consuming and imprecise if done manually. Recently, GlycoSearch software was developed to facilitate the analysis and interpretation of glycan array data based on two previously developed methods, Motif Segregation and Outlier Motif Analysis. Here, the principles behind this method and the use of this new tool for mining glycan array data are described. The automated, objective, and precise analysis of glycan array data should enhance the value of these data for a broad range of research applications. Curr. Protoc. Chem. Biol. 5:157‐169 © 2013 by John Wiley & Sons, Inc.

Keywords: glycobiology; glycan array; glycan motif; lectin

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Analyzing Glycan Array Data Using GlycoSearch
  • Alternate Protocol 1: Refining Motif Interpretation Using Combined and Excluded Motifs
  • Alternate Protocol 2: Refining Motif Interpretation Using Outlier Analysis
  • Alternate Protocol 3: Testing New Motifs
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Analyzing Glycan Array Data Using GlycoSearch

  Materials
  • GlycoSearch software (freely available from the authors)
  • Glycan array data (tab‐delimited text file or a Microsoft Excel workbook)
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Figures

Videos

Literature Cited

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Internet Resources
  Consortium for Functional Glycomics (CFG): http://www.functionalglycomics.org
  This site provides access to resources and information assembled by the CFG. Data from thousands of glycan array experiments and other types of experiments are available, along with fundamental biological information, links to additional resources, and descriptions of reagents that are available through the consortium.
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