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Tabulation

Select Glycan Array Data

Array data overview page will be displayed by selecting Glycan Array Data from Project explorer area.

Display Glycan Array Data – Master table

The tabulation results page will be displayed by clicking Show Master Table button in the overview page.

This is a screen shot of the results page. This result view includes Parameter Setting View, Master Table, Filter, Sorter and Plot View sections.

  1. Parameter – Users are able to adjust the mode of presentation of the scan data in the table according to Fluorophore, Scan Power, Statistical Method or Signal Type by clicking Recalculate button.
  2. Master table – The scan data are visualised in a table with or without glycan sequences. The format of glycan sequences (text or image) can be selected from ‘Preference’ in the main menu. Users are also able to edit the number of columns to show in the master table by right-clicking the table header and opening the column chooser.
  3. Filter and Sorter section – Users are able to filter and sort by the number of particular monosaccharides, by their linkage and by the presence of certain motifs such as sLex.
  4. Functional buttons – Users are able to generate a chart by clicking Creating Histogram button (left). Click Save Data button (middle) to save the tabulation result with filtering and sorting conditions. And users can export the tabulation results to an Excel file by clicking Export button (right).
  5. Histogram view – A chart will be drawn automatically based on the results in table.



Histogram charts

Users are able to generate a histogram chart form the tabulation result view.

  1. Functional buttons – Users are able to generate a chart by clicking Creating Histogram button (left). Click Save Data button (middle) to save the tabulation result with filtering and sorting conditions. And users can export the tabulation results to an Excel file by clicking Export button (right).
  2. Histogram view – A chart will be drawn automatically based on the results in table.



Users can change the range of view by

  • Ctrl + ↑(scroll up): Zoom in
  • Ctrl + ↓(scroll up): Zoom in
  • Right click
    • Adjust Axis Range
      • Adjust Axis Range: reset the view range
      • Adjust X Axis Range: fit the chart with x axis
      • Adjust Y Axis Range: fit the chart with y axis
    • Zoom In
      • Zoom In
      • Zoom In X Axis
      • Zoom In Y Axis
    • Adjust Zoom Out
      • Zoom Out
      • Zoom Out X Axis
      • Zoom Out Y Axis
    • Save As… : Save the chart as an image file
    • Properties… : Users can change the property of the chart such as the font colour, grid line type and labels.


A screenshot of a property window.

Filtering and sorting functions

Users can set the filtering and sorting condition from the Filter and Sorter Section.

  1. AND or OR selection: AND and OR operation to combine multiple filtering conditions to narrower the data.
  2. Pull-down menu for filtering and sorting items. Users can add (or remove) the selected item to (from) the table.
  3. Filter: the name of the selected item
    Description: a brief description of the item
    Include: a check box to select “include” the item in the table result view (checked) or “exclude” (unchecked)
    Selection: if the item has a sub-category (e.g. N-glycan), users need to select the item from here.
    Min and Max: if the item is a monosaccharide and the number of branch, users can enter the minimum and maximum value
  4. Apply Filter: operate the filtering using the selected items
    Reset filters: reset all the filtering conditions from the table result view
  5. Sorter: the name of the selected item
    Description: a brief description of the item
    Sort Order: users can select the sorting order (Asc or Desc)

Items used in the filtering and sorting function


Users can filter and sort the tabulation results by:

  • Average intensity values per glycan probe level
    Filtering example: When glycan probes are printed in 2 levels (2 and 5 fmol/spot), users can cut off glycan probes which average intensity values are less than 500 at lower (or higher) level.
  • Backbone type1
    • Group A: Gal, Glc, Lac, LacNac
    • Group B: LNnT, LNT
    • Group C: polylactosamine (linear, branched)
    • Group D: N-glycan
    • Group E: Ganglioside related
    • Group F: O-glycan
    • Group G: Polysialyl
    • Group H: GAG (sub types for GAG)
    • Group I: Other homo-oligomers
    • Group J: Miscellaneous
  • Slide name
  • Subarray name
  • Probe name
  • Probe position
  • Probe tag
  • Monosaccharides (Table 1)
  • Charge of monosaccharide (acidic monosaccharides, phosphate and sulfate, Table 1)
  • Terminal monosaccharides (monosaccharides which locate at the non-reducing end, Table 1)
  • Number of residues (total number of monosaccharide residues, phosphate or sulfate groups in a glycan probe)
  • Number of Branches
  • Glycan substructures and motifs (Tables 2–8)




Monosaccharides and modifications


Table 1 incudes the monosaccharides from Symbol Nomenclature for Glycans (SNFG)2 and chemically modified sugars in Glycosciences Laboratory. Monosaccharides which were not translated into GlycoCT format3 are not included in this table.


Table 1. Monosaccharides and modifications available in the filtering and sorting function
Name Charged Terminal Symbol Name Charged Terminal Symbol Name Charged Terminal Symbol
1 Glc ✓ 25 GlcA ✓ ✓ 49 Lyx
2 Man ✓ 26 ManA ✓ 50 Xyl ✓
3 Gal ✓ 27 GalA ✓ 51 Rib
4 Gul 28 GulA ✓ 52 Kdn ✓
5 Alt 29 AltA ✓ 53 Neu5Ac ✓
6 All 30 AllA ✓ 54 Neu5Gc ✓
7 Tal ✓ 31 TalA ✓ 55 Neu ✓
8 Ido 32 IdoA ✓ ✓ 56 Sialic acid ✓
9 GlcNAc ✓ 33 Qui (D-Qui) 57 Bac ✓
10 ManNAc 34 Rha ✓ 58 Kdo ✓
11 GalNAc ✓ 35 6dGul 59 MurNAc ✓
12 GulNAc 36 6dAlt 60 MurNGc ✓
13 AltNAc 37 6dTal 61 Mur ✓
14 AllNAc 38 Fuc ✓ 62 Api
15 TalNAc 39 QuiNAc 63 Fru
16 IdoNAc 40 RhaNAc 64 Tag
17 GlcN 41 6dAltNAc 65 Sor
18 ManN 42 6dTalNAc 66 Psi
19 GalN 43 FucNAc 67 aMan4
20 GulN 44 Tyv 68 dUA5 ✓
21 AltN 45 Abe 69 Quv6 ✓
22 AllN 46 Par 70 Phosphate ✓
23 TalN 47 Col 71 Sulfate ✓
24 IdoN 48 Ara ✓




Glycan substructures and motifs


The tables below list the substructures and motifs based on the mammalians available in the filtering and sorting function.
The ’Non-grouped’ table (Table 2) lists substructures and motifs which users can select directory from the filtering drop-down list.
The items in Tables 3 – 8 are substructures and motifs which are categorised in each group. Users needs to select the group name from the filtering and sorting drop-down list, then, select the motif name from the Selection list.


Filtering


For example, if a user wants to use “Blood Group A” (GalNAc α1-3 (Fuc α1-2) Gal) for filtering, the user can just select the item in the drop-down menu.
If a user wants to use “Hyaluronic acid” (GlcA β1-3 GlcNAc), which is categorised in GAG Type (Table 7), the user needs to: (1) select GAG Types and (2) select Hyaluronic acid from the sub-selection.

Sorting


For example, if a user wants to order by “Neu5Ac” in ascending, the user can just select “Neu5Ac” from the sorting drop-down menu and select ‘Asc’ from the Order selection.
If a user selects “Sialyl linkage” type (Table 5) from the drop-down menu, the table will be sorted based on the sialyl linkage types automatically.
The image below is the screenshot of sorting results. The glycan probes are first sorted by the number of Neu5Ac and then sorted by the Sialyl linkage (first item in the order is Neu5Ac α2-3 and second item is Neu5Ac α2-6).

Non-capped motifs

Table 2. Non-capped substructures and motifs
Name Sequence Structure
1 Lewis A Galβ1-3(Fucα1-4)GlcNAc
2 Lewis B Fucα1-2Galβ1-3(Fucα1-4)GlcNAc
3 Lewis X Galβ1-4(Fucα1-3)GlcNAc
4 Lewis Y Fucα1-2Galβ1-4(Fucα1-3)GlcNAc
5 Sialyl-Lewis A Neu5Acα2-3Galβ1-3(Fucα1-4)GlcNAc
6 Sialyl-Lewis X Neu5Acα2-3Galβ1-4(Fucα1-3)GlcNAc
7 Blood Group A GalNAcα1-3(Fucα1-2)Gal
8 Blood Group B Galα1-3(Fucα1-2)Gal
9 Blood Group O/H Fucα1-2Gal
10 Gal-Gal Galα1-3Gal
11 Sda GalNAcβ1-4(Neu5Acα2-3)Gal
12 Lac-Di-NAc GalNAcβ1-4GlcNAc
13 LacNAc (type 1) Galβ1-3GlcNAc
14 LacNAc (type 2) Galβ1-4GlcNAc




N-glycan

Table 3. N-glycan type
Name Sequence Structure
1 High-mannose Manα1-?Manα1-3(Manα1-?Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAc
2 Hybrid GlcNAcβ1-?Manα1-3(Manα1-?Manα1-6)Manβ1-4GlcNAcβ1-4GlcNAc
3 Complex GlcNAcβ1-?Manα1-6(GlcNAcβ1-?Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc
*’?’ indicates any linkage number




O-glycan (mucin type) core structures

Table 4. O-glycan group
Name Sequence Structure
1 Core1 Galβ1-3GalNAc
2 Core1 GlcNAcβ1-6(Galβ1-3)GalNAc
3 Core3 GlcNAcβ1-3GalNAc
4 Core4 GlcNAcβ1-6(GlcNAcβ1-3)GalNAc
5 Core5 GalNAcα1-3GalNAc
6 Core6 GlcNAcβ1-6GalNAc
7 Core7 GalNAcα1-6GalNAc
8 Core8 Galα1-3GalNAc




Sialyl linkages

Table 5. Sialyl linkage group
Name Sequence
1 Sia 2,2 termini Siaα2-2
2 Sia 2,3 termini Siaα2-3
3 Sia 2,6 termini Siaα2-6
4 Sia 2,8 termini Siaα2-8
5 Sia 2,9 termini Siaα2-9
6 Sia 2,3:2,6 termini α3 and α6 termini
7 Sia 2,3:2,8 termini α3 and α8 termini




Glycolipid types

Table 6. Glycolipid group 7
Name Sequence Structure
1 Lacto Galβ1-3GlcNAcβ1-3Galβ1-4Glc
2 Neolacto Galβ1-4GlcNAcβ1-3Galβ1-4Glc
3 Ganglio Galβ1-3GalNAcβ1-4Galβ1-4Glc
4 Globo GalNAcβ1-3Galα1-4Galβ1-4Glc
5 Isoglobo GalNAcβ1-3Galα1-3Galβ1-4Glc
6 Arthro GalNAcβ1-4GlcNAcβ1-3Manβ1-4Glc
7 Mollu GlcNAcβ1-2Manα1-3Manβ1-4Glc




GAG types

Table 7. GAG group. A modified version of GAG types in Essential Glycobiology 8
Name Sequence of typical disaccharide units Structure
1 Hyaluronic acid GlcAβ1-3GlcNAcβ1-
2 Keratan sulfate (mono) Galβ1-4GlcNAc(6S)β1-
3 Keratan sulfate (di) Gal(6S)β1-4GlcNAc(6S)β1-
4 Chondroitin sulfate-A GlcAβ1-3GalNAc(4S)β1-
5 Chondroitin sulfate-C GlcAβ1-3GalNAc(6S)β1-
6 Chondroitin sulfate-D GlcA(2S)β1-3GalNAc(6S)β1-
7 Chondroitin sulfate-E GlcAβ1-3GalNAc(4S,6S)β1-
8 Dermatan sulfate IdoAα1-3GalNAc(4S)β1-
9 Heparan sulfate (non-sulfated) GlcAβ1-4GlcNAcα1-
10 Heparin IdoA(2S)α1-4GlcNS(6S)α1-




Glucosyl linkage

Table 8. Glucosyl linkage type
Name Sequence
1 Glc alpha 2 Glcα1-2
2 Glc alpha 3 Glcα1-3
3 Glc alpha 4 Glcα1-4
4 Glc alpha 4,6 Combination of α4 and α6 linkage (linear)
5 Glc alpha 6 Glcα1-6
6 Glc beta 2 Glcβ1-2
7 Glc beta 3 Glcβ1-3
8 Glc beta 3,4 Combination of β3 and β4 linkage (linear)
9 Glc beta 3/6 Contains β3 and β6 branched
10 Glc beta 4 Glc β1-4
11 Glc beta 6 Glc β1-6






Note

  1. This classification is found to be useful in report writing in Glycosciences Laboratory
  2. Updates to the Symbol Nomenclature for Glycans guidelines, Glycobiology 29:620-624, 2019
  3. GlycoCT—a unifying sequence format for carbohydrates, Carbohydrate Research 343: 2162-2171, 2008
  4. Anhydromannose
  5. Δ4,5-unsatu-rateduronicacid)
  6. L-quinovose (6-deoxy-L-glucose)
  7. Chapter 11, Glycosphingolipids, Essentials of Glycobiology. 3rd edition. Varki A, Cummings RD, Esko JD, et al., editors. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2015-2017.
  8. Chapter 17, Proteoglycans and Sulfated Glycosaminoglycans Essentials of Glycobiology. 3rd edition. Varki A, Cummings RD, Esko JD, et al., editors. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2015-2017.



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