Glycosciences Laboratory

Data storage

data storage functions

Storing carbohydrate microarray data from different array formats and related array-specific metadata

Users can store a wide range of microarray experiment related information such as project details, collaborators, glycan binding sample metadata, experiment protocols, array geometry, glycan microarray scan data and processed data. Most of the information is compliant with MIRAGE Glycan Microarray Guidelines.

For example, in the glycan binding sample (Analyte) metadata entry page, users can record the following.

Origin of the sample (sample type) by selecting: natural, recombinant or synthetic
Information on a database entry of the sample such as PDB ID
Purity and quality control parameters

In the experiment design tool, users can record the experiment procedures with parameters such as overlay steps of the sample on the array and incubation steps with or without pre-complexation of samples.

Array layout (array geometry), including glycan probes with printing locations and concentrations or doses, can be recorded in the software. Users need to select an array layout from the pre-stored array layout to generate processed data including average binding intensities.

Data presentation

Presentation of processed data as tables and charts with filtering and sorting functions

After selecting the array layout, the binding intensities need to be uploaded in GenePix Result or Proscan file.

Users have options for data processing for presentation. These include:

Calculation method for averageing the intensity values with or without outlier elimination
Binding signals:

Median - the intensity values under column header 'Median' in the uploaded scan file
Mean - the intensity values under column header 'Mean' in the uploaded scan file
Median minus background (Median-B) - the intensity values under column header 'Median-B' in the uploaded scan file
Mean minus background (Mean-B) - the intensity values under column header 'Mean-B' in the uploaded scan file
Median minus background (MedianS-B) - the intensity values after substracting the values in Background from Median
Mean minus background (MeanS-B)- the intensity values after substracting the values in Background from Median

The data thus are presented as tables, charts and heatmaps. Users can filter and sort the processed glycan microarray data based on monosaccharide contents, substructure, motifs and backbone types stored in CarbArrayART. Seventy-eight types of monosaccharides and seventy-two motifs are adapted from Symbol Nomenclature for Glycans and Mark’s software tools.

Data reporting

Reporting data compliant with MIRAGE guidelines

Results tables and metadata can be exported as Excel files where glycan sequences can be visualized in multiple formats including SNFG symbolic, Oxford symbol nomenclature and Text format. Glycan binding sample and experiment metadata can be exported as Word and PDF files. The metadata are compliant with MIRAGE.