Preparing glycomics data for robust statistical analysis with GlyCompareCT

Yujie Zhang; Sridevi Krishnan; Bokan Bao; Austin W T Chiang; James T Sorrentino; Song-Min Schinn; Benjamin P Kellman; Nathan E Lewis

doi:10.1016/j.xpro.2023.102162

Preparing glycomics data for robust statistical analysis with GlyCompareCT

STAR Protoc. 2023 Mar 13;4(2):102162. doi: 10.1016/j.xpro.2023.102162. Online ahead of print.

Authors

Yujie Zhang¹, Sridevi Krishnan², Bokan Bao³, Austin W T Chiang², James T Sorrentino³, Song-Min Schinn³, Benjamin P Kellman⁴, Nathan E Lewis⁵

Affiliations

¹ Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA.
² Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA.
³ Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA.
⁴ Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Augment Biologics, 9450 SW Gemini Dr. #46664, Beaverton, OR 97008, USA. Electronic address: benjamin.kellman@gmail.com.
⁵ Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0760, La Jolla, CA 92093, USA. Electronic address: nlewisres@ucsd.edu.

Abstract

GlyCompareCT is a portable command-line tool to facilitate downstream glycomic data analyses, by addressing data inherent sparsity and non-independence. Inputting glycan abundances, users can run GlyCompareCT with one line of code to obtain the abundances of a minimal substructure set, named glycomotif, thereby quantifying hidden biosynthetic relationships between measured glycans. Optional parameters tuning and annotation are supported for personal preference. For complete details on the use and execution of this protocol, please refer to Bao et al. (2021).¹.

Keywords: Bioinformatics; Molecular Biology; Systems Biology.

Abstract

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