Automated Analysis report for RCA Vector NCFG

Array Chart

Figure 1. Barcharts of raw glycan binding data. Glycans are grouped by family (automatically if not provided) and sorted by binding strength. Mouseover to see glycan structures.

Primary Motifs

Figure 2. Boxplots of glycans grouped by primary motif. Individual points are glycans. Mouseover to see glycan structures.
Primary Motif ID Motif Graphic Structure Relative Binding Number of Glycans
A A0p 0.98 36
B B0p 1.00 7
C C0p 0.61 24
D D0p 0.65 6
E E0p 0.45 5
0 0.00 520
Figure 2. Boxplots of glycans grouped by primary motif. Individual points are glycans. Mouseover to see glycan structures.
Primary Motif ID Motif Graphic Structure Relative Binding Number of Glycans
A A0p 1.00 36
B B0p 0.58 7
C C0p 0.12 24
D D0p 0.23 6
E E0p 0.24 5
0 0.00 520
Figure 2. Boxplots of glycans grouped by primary motif. Individual points are glycans. Mouseover to see glycan structures.
Primary Motif ID Motif Graphic Structure Kd Number of Glycans
A A0p 3.48122 35
B B0p 6.12955 7
C C0p 22.9437 22
D D0p 8.77411 6
E E0p 10.2669 3
0 64.5545 46

All Motifs

Figure 3. Boxplots of glycans grouped by motif. Individual points are glycans. Mouseover to see glycan structures.
Motif ID Nearest Common Name (Accuracy%**) Motif Graphic Structure Relative Binding Number of Glycans P-Value***
A3 Type 2 TriLacNAc/i Antigen (97%) A3p 1.00 4 0.000
A0* Terminal Type 2 LacNAc Type 2 TriLacNAc/i Antigen (99%) A0p 0.85 9 0.000
A1 Terminal Type 2 LacNAc Terminal N-Actyl Hexosamine (99%) A1p 0.76 13 0.000
A2 Terminal Type 2 LacNAc Biantennary N-Glycan (97%) A2p 0.65 10 0.000
B0 a6 Sialyl Type 2 LacNAc Bisecting N-Glycan (99%) B0p 0.80 7 0.000
C0 Terminal Type 2 LacNAc (93%) C0p 0.49 24 0.000
D0 Terminal 6' Sulfated Galactose (99%) D0p 0.51 6 0.000
E0 Type 2 DiLacNAc 5-Acetyl Neuramic Acid (98%) E0p 0.36 5 0.000
0 Non-Binders (100%) 0.00 520 NA
Figure 3. Boxplots of glycans grouped by motif. Individual points are glycans. Mouseover to see glycan structures.
Motif ID Nearest Common Name (Accuracy%**) Motif Graphic Structure Relative Binding Number of Glycans P-Value***
A3 Type 2 TriLacNAc/i Antigen (97%) A3p 1.00 4 0.000
A0* Terminal Type 2 LacNAc Type 2 TriLacNAc/i Antigen (99%) A0p 0.57 9 0.000
A2 Terminal Type 2 LacNAc Biantennary N-Glycan (97%) A2p 0.47 10 0.000
A1 Terminal Type 2 LacNAc Terminal N-Actyl Hexosamine (99%) A1p 0.28 13 0.000
B0 a6 Sialyl Type 2 LacNAc Bisecting N-Glycan (99%) B0p 0.28 7 0.000
C0 Terminal Type 2 LacNAc (93%) C0p 0.06 24 0.001
D0 Terminal 6' Sulfated Galactose (99%) D0p 0.11 6 0.001
E0 Type 2 DiLacNAc 5-Acetyl Neuramic Acid (98%) E0p 0.12 5 0.001
0 Non-Binders (100%) 0.00 520 NA
Figure 3. Boxplots of glycans grouped by motif. Individual points are glycans. Mouseover to see glycan structures.
Motif ID Nearest Common Name (Accuracy%**) Motif Graphic Structure Kd Number of Glycans P-Value***
A3 Type 2 TriLacNAc/i Antigen (97%) A3p 0.109604 4 0.000
A0* Terminal Type 2 LacNAc Type 2 TriLacNAc/i Antigen (99%) A0p 3.27849 9 0.000
A2 Terminal Type 2 LacNAc Biantennary N-Glycan (97%) A2p 4.17136 9 0.000
A1 Terminal Type 2 LacNAc Terminal N-Actyl Hexosamine (99%) A1p 4.18121 13 0.000
B0 a6 Sialyl Type 2 LacNAc Bisecting N-Glycan (99%) B0p 6.12955 7 0.000
C0 Terminal Type 2 LacNAc (93%) C0p 22.9437 22 0.000
D0 Terminal 6' Sulfated Galactose (99%) D0p 8.77411 6 0.000
E0 Type 2 DiLacNAc 5-Acetyl Neuramic Acid (98%) E0p 10.2669 3 0.001
0 Non-Binders (100%) 64.5545 46 NA

*Motif indicates the remaining glycans not matched by motifs which are a subset. Motif definition needs to be taken in the context of the model.

**Accuracy describes the consistency between common-name definition of the motif and the formal, text-based definition of the motif, in terms of percent agreement in the glycans containing the two motifs. Common Name label definitions given here.

***P-Value refers to difference from Non-Binders with multiple testing correction (Dunnet’s Test)

Motifs with a red motif ID fail to show a logistic response to protein concentration in the range of concentrations analyzed. These motifs may be nonbinding motifs (motifs which define nonbinding exceptions) or simply fail to fit. Nonbinding motifs are determined based on concentration dependent response when available or the average binding of non-motif glycans otherwise.

Motif Intensity Maps

Figure 4. Glycan intensity and motif distribution plot. The top half of the plot presents the observed glycan binding intensity of various glycans used in the array over their rank binding intensity; only the top glycans are shown. The second plot indicates the position of glycans containing the various motifs in the top plot with a yellow tick.

Treemap Diagram

*Motif indicates the remaining glycans not matched by motifs which are a subset. Motif definition needs to be taken in the context of the model.

Figure 5. Treemap of glycan binding grouped by motif and family structure. The model structure can be represented as nested boxes where box size is proportional to the number of glycans with the motif and color changes with change in average relative binding of glycans with the motif. Only three layers of data splitting are included here, though further splitting may be possible.

Model Diagram

*Motif matches the remaining glycans not matched by earlier motifs in the model.

Figure 6. Tree representation of the regression tree model trained on array data. Data flows through the tree (top-down) and is split by the various motifs. The motif used the split the data at each point has the id “family+split number” except when further split. In the case of futher splits the id of the motif used to split the data is denoted with an asterisk.

Binding Curves

Figure 7. Logistic curves fit to average motif binding and glycan binding. Curves are fit with as many parameters as possible given the data. All curves are based on the logistic curve with a fixed intercept of 0. Mouse-over to view curve info and highlight glycans/motifs on the other plot.

Figure 8. Scatterplots of logistic curve parameters for glycans (points) and motifs (text).

Motif Details

Motif ID Motif Graphic   Motif Full Graphic Kd Asymptote Slope Motif Text
A1 A1p A1Full 2.042 37917 1 {<2f3f4f6f>GalB1-4<3f6f>GlcNAcB1-<2or3><4f><GalorMan>?1-<3or4or6><2f><GlcNAcorMan>B1-<2or4><3f6f><GlcNAcorMan>?1-<3or4><2f><GlcNAcorMan>A}
A2 A2p A2Full 0.364 28275 1 {<2f3f4f6f>GalB1-4<3f6f>GlcNAcB1-<2or3><4f6f><GalorMan>?1-<3or4or6><2f><GlcNAcorMan>B1-<2or4><6f><GlcNAcorMan>?1-<3or4><2f><GlcNAcorMan>B}
A3 A3p A3Full 0.000 43137 1 {<2f3f4f6f>GalB1-4<3f6f>GlcNAcB1-3<2f4f6f>GalB1-4<3f6f>GlcNAcB1-3<2f4f6f>GalB1-4<3f6f>GlcNAcB1-3<2f4f6f>GalB1-4<3f6f>GlcNAcB1-3<2f4f6f>GalB}
A0 A0p A0Full 0.475 36897 1 {<2f3f4f6f>GalB1-4<3f6f>GlcNAcB1-<2or3><4f><GalorMan>?1-<3or4or6><2f><GlcNAcorMan>B1-<2or3or4><6f><GalorGlcNAcorMan>?}
B0 B0p B0Full 2.278 40638 1 {<4f6f8f>Neu5AcA2-6<2f3f4f>GalB1-4<3f6f>GlcNAcB1-<2or4><3f>ManA1-6(<4f6f8f>Neu5AcA2-6<2f3f4f>GalB1-4<3f6f>GlcNAcB1-2<3f6f>ManA1-3)<2f>ManB1-4<3f6f>GlcNAcB1-4<3f6f>GlcNAcB}
C0 C0p C0Full 21.814 65536 1 {<2f3f4f6f>GalB1-4<3f6f>GlcNAc?1-<3or6><2f4f><GalorGalNAc>?}
D0 D0p D0Full 5.909 34609 1 {(6S)<2f3f4f><GalorGalNAc>B1-4<1f2f3f><GlcorGlcNAc>B}
E0 E0p E0Full 2.722 19735 1 {{<3f6f8f><GlcNAcorNeu5Ac>?<1or2>-<3or6><2f4f>GalB1-4<3f6f>GlcNAcB1-3<2f4f6f>GalB1-4<3f6f>GlcNAcB1-2<3f4f6f>ManA1-6(<3f6f8f><GlcNAcorNeu5Ac>?<1or2>-<3or6><2f4f>GalB1-4<3f6f>GlcNAcB1-3<2f4f6f>GalB1-4<3f6f>GlcNAcB1-2<3f4f6f>ManA1-3)<2f4f>ManB1-4<3f6f>GlcNAcB1-4<3f6f>GlcNAcB}N} {Spacer:Asn}

See Symbol Nomenclature for Glycans (SNFG) for complete key: https://www.ncbi.nlm.nih.gov/glycans/snfg.html