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2 RELATED WORK
No tools have been found in the literature that fill all
the gaps in microarray analysis detected by the end-
users involved in the project, as most of the scientific
efforts in this field are put on developing better and
more diverse microarrays instead of developing tools
for analysis.
Almost every commercially available software for
microarray analysis focus on gene or peptide
microarrays, which is not useful for lectin and glycan
analyses. Also, some other tools were detected that do
focus on glycans and lectins, but they analyse data
coming from other technologies, such as mass
spectrometry (Goldberg et. al., 2005; Maass et. al.,
2007), or focus more on the molecules structure and
their representation (Aoki-Kinoshita, 2008), which is
still not the target of this project.
Nevertheless, two software developed specifically
for glycan analysis were detected. The first software
is a stand-alone program composed by a suite of
modules to store, retrieve and display glycan
microarray data. It provides an internal database to
store all the information related to the glycans, their
associated proteins and the experimental data; it also
provides different tools for data visualization, sorting
and filtering; and finally, it includes modules for
automatic plots generation (Stoll and Feizi, 2010).
The second tool is called GLAD (Glycan Array
Dashboard), and it is a web-based tool that provides
functions to visualize and analyse glycan microarray
data, and also compare information coming from
different experiments. It has a module for basic plot
generation (i.e. bar charts) for single-sample data, or
complex plot generation for comparison of samples.
This tool also includes a module for data
normalization between samples, necessary for
comparison (Mehta and Cummings, 2019).
However, none of the described programs fulfil all
the needs of the project, according to the participating
end-users. The main drawback is that the software
interfaces are not as intuitive and easy-to-use as
desired, so the different included functionalities are
not easy to exploit. Another downside is that these
programs were designed strictly for glycan array
analysis, so they do not work with lectin arrays, which
is one of the main requirements. Therefore, the best
approach was to create a tool from scratch and include
all the desired functionalities gradually.
3 LECTIN AND GLYCAN
MICROARRAYS
3.1 Lectins, Glycans and Glycoproteins
Lectins are a group of proteins that present certain
binding behaviour toward carbohydrates, specifically
soluble carbohydrates and the residues of
glycoconjugates (i.e. glycans). These proteins bind
saccharides reversibly and with high specificity, but
can have more than one-binding size along a single
molecule, so they can be specific for more than one
sugar molecule at once.
Lectins can be found commonly in nature: in
plants, animals and bacteria; and they have been
associated with a broad set of functions depending on
where they are found. It is interesting to highlight
their role as recognition molecules in cell-molecule
and cell-cell interactions, affecting a wide range of
cellular events (Lis and Sharon, 1998).
These molecules do not only have a role in nature,
but many different usages have been given to them in
clinical and experimental settings, for example, in
blood typing, histochemical analyses and
biomolecules purification.
Another important group of biomolecules are the
glycans. In general, glycan is considered as a
synonym for polysaccharide, which are “compounds
consisting of a large number of monosaccharides
linked glycosidically” (IUPAC, 1997), usually
formed by more than 10 sugar residues. Nevertheless,
in this context the term will be associated to the
saccharide portion of a glycoconjugate molecule,
which are molecules of carbohydrate bonded to other
compounds (i.e. glycoprotein, glycolipid or
proteoglycan) (Dwek, 1996).
Historically, it was believed that the solely
function of sugar molecules was being a source of
energy, but now it is well-known that they have many
other functions in the biological systems. Glycomics
is the science that focuses on studying the glycome of
the organisms, trying to define structures and
functions of carbohydrates in nature.
Glycoproteins are formed through direct
interactions between glycans and proteins. The
glycans of these molecules can also be attached to
other macromolecules, which indirectly control the
glycoprotein conformation, stability, turnover,
oligomerization and cell surface resident time
(Cummings and Pierce, 2014).
It is important to highlight that the proteins
conforming the glycoproteins are not lectins. Lectins
may temporary bind the sugar fragment of
glycoproteins in order to execute certain functions,
SugarArray: A User-centred-designed Platform for the Analysis of Lectin and Glycan Microarrays
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