TY - JOUR
T1 - CarbArrayART
T2 - A new software tool for carbohydrate microarray data storage, processing, presentation, and reporting
AU - Akune, Yukie
AU - Arpinar, Sena
AU - Silva, Lisete M.
AU - Palma, Angelina S.
AU - Tajadura-Ortega, Virginia
AU - Aoki-Kinoshita, Kiyoko F.
AU - Ranzinger, Rene
AU - Liu, Yan
AU - Feizi, Ten
N1 - Publisher Copyright:
© 2022 The Author(s) 2022. Published by Oxford University Press.
This project is supported by Wellcome Trust Biomedical Resource grants (WT099197/Z/12/Z, 108430/Z/15/Z and 218304/Z/19/Z); March of Dimes European Prematurity Research Centre grant 22-FY18-82 and NIH Commons Fund 1U01GM125267-01.
PY - 2022/7
Y1 - 2022/7
N2 - Glycan microarrays are essential tools in glycobiology and are being widely used for assignment of glycan ligands in diverse glycan recognition systems. We have developed a new software, called Carbohydrate microArray Analysis and Reporting Tool (CarbArrayART), to address the need for a distributable application for glycan microarray data management. The main features of CarbArrayART include: (i) Storage of quantified array data from different array layouts with scan data and array-specific metadata, such as lists of arrayed glycans, array geometry, information on glycan-binding samples, and experimental protocols. (ii) Presentation of microarray data as charts, tables, and heatmaps derived from the average fluorescence intensity values that are calculated based on the imaging scan data and array geometry, as well as filtering and sorting functions according to monosaccharide content and glycan sequences. (iii) Data export for reporting in Word, PDF, and Excel formats, together with metadata that are compliant with the guidelines of MIRAGE (Minimum Information Required for A Glycomics Experiment). CarbArrayART is designed for routine use in recording, storage, and management of any slide-based glycan microarray experiment. In conjunction with the MIRAGE guidelines, CarbArrayART addresses issues that are critical for glycobiology, namely, clarity of data for evaluation of reproducibility and validity.
AB - Glycan microarrays are essential tools in glycobiology and are being widely used for assignment of glycan ligands in diverse glycan recognition systems. We have developed a new software, called Carbohydrate microArray Analysis and Reporting Tool (CarbArrayART), to address the need for a distributable application for glycan microarray data management. The main features of CarbArrayART include: (i) Storage of quantified array data from different array layouts with scan data and array-specific metadata, such as lists of arrayed glycans, array geometry, information on glycan-binding samples, and experimental protocols. (ii) Presentation of microarray data as charts, tables, and heatmaps derived from the average fluorescence intensity values that are calculated based on the imaging scan data and array geometry, as well as filtering and sorting functions according to monosaccharide content and glycan sequences. (iii) Data export for reporting in Word, PDF, and Excel formats, together with metadata that are compliant with the guidelines of MIRAGE (Minimum Information Required for A Glycomics Experiment). CarbArrayART is designed for routine use in recording, storage, and management of any slide-based glycan microarray experiment. In conjunction with the MIRAGE guidelines, CarbArrayART addresses issues that are critical for glycobiology, namely, clarity of data for evaluation of reproducibility and validity.
KW - glycan microarray data management
KW - glycan microarray data presentation
KW - glycan microarray data storage
KW - glycan microarray software
KW - glycoinformatics
UR - http://www.scopus.com/inward/record.url?scp=85131903191&partnerID=8YFLogxK
U2 - 10.1093/glycob/cwac018
DO - 10.1093/glycob/cwac018
M3 - Article
C2 - 35352122
AN - SCOPUS:85131903191
SN - 0959-6658
VL - 32
SP - 552
EP - 555
JO - Glycobiology
JF - Glycobiology
IS - 7
ER -