Automated Analysis report for SSA Investigator Provided CFG

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 0.43 27
B B0p 1.00 1
C C0p 0.27 6
D D0p 0.23 4
E E0p 0.02 23
0 0.00 283
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 0.55 27
B B0p 1.00 1
C C0p 0.19 6
D D0p 0.17 4
E E0p 0.03 23
0 0.00 283
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 27
B B0p 0.90 1
C C0p 0.66 6
D D0p 0.71 4
E E0p 0.39 23
0 0.00 283
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 2.79397 18
B B0p 0.379677 1
C C0p 7.75429 5
D D0p 10 3
E E0p 1.89675 22
0 8.22797 16

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***
A5* Terminal Type 2 LacDiNAc (100%) A5p 1.00 2 0.000
A2 Terminal N-Actyl Galactosamine (94%) A2p 0.56 5 0.000
A0* Terminal N-Actyl Galactosamine (94%) A0p 0.49 5 0.000
A3 Terminal Type 2 LacDiNAc (99%) A3p 0.15 1 0.221
A1 Blood Group A (100%) A1p 0.01 7 1.000
A6 Terminal N-Actyl Galactosamine 5-Acetyl Neuramic Acid (100%) A6p -0.00 6 1.000
A4 Terminal N-Actyl Galactosamine (92%) A4p -0.01 1 1.000
B0 O-GalNAc Core 6 (100%) B0p 0.65 1 0.000
C0 Blood Group H (93%) C0p 0.17 6 0.000
D0 Terminal Mannose (96%) D0p 0.15 4 0.000
E0 E0p 0.01 23 0.988
0 Non-Binders (100%) 0.00 283 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***
A5* Terminal Type 2 LacDiNAc (100%) A5p 1.00 2 0.000
A2 Terminal N-Actyl Galactosamine (94%) A2p 0.64 5 0.000
A0* Terminal N-Actyl Galactosamine (94%) A0p 0.51 5 0.000
A3 Terminal Type 2 LacDiNAc (99%) A3p 0.12 1 0.697
A6 Terminal N-Actyl Galactosamine 5-Acetyl Neuramic Acid (100%) A6p 0.01 6 1.000
A1 Blood Group A (100%) A1p 0.00 7 1.000
A4 Terminal N-Actyl Galactosamine (92%) A4p -0.02 1 1.000
B0 O-GalNAc Core 6 (100%) B0p 0.53 1 0.000
C0 Blood Group H (93%) C0p 0.10 6 0.014
D0 Terminal Mannose (96%) D0p 0.09 4 0.174
E0 E0p 0.02 23 0.985
0 Non-Binders (100%) 0.00 283 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***
A5* Terminal Type 2 LacDiNAc (100%) A5p 1.00 2 0.000
A2 Terminal N-Actyl Galactosamine (94%) A2p 0.79 5 0.000
A0* Terminal N-Actyl Galactosamine (94%) A0p 0.57 5 0.000
A6 Terminal N-Actyl Galactosamine 5-Acetyl Neuramic Acid (100%) A6p 0.05 6 0.952
A3 Terminal Type 2 LacDiNAc (99%) A3p 0.03 1 1.000
A1 Blood Group A (100%) A1p -0.00 7 1.000
A4 Terminal N-Actyl Galactosamine (92%) A4p -0.04 1 1.000
B0 O-GalNAc Core 6 (100%) B0p 0.30 1 0.062
C0 Blood Group H (93%) C0p 0.22 6 0.000
D0 Terminal Mannose (96%) D0p 0.24 4 0.000
E0 E0p 0.13 23 0.000
0 Non-Binders (100%) 0.00 283 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***
A5* Terminal Type 2 LacDiNAc (100%) A5p 0.293086 2 0.087
A3 Terminal Type 2 LacDiNAc (99%) A3p 0.360382 1 0.414
A0* Terminal N-Actyl Galactosamine (94%) A0p 2.12066 4 0.070
A2 Terminal N-Actyl Galactosamine (94%) A2p 2.15747 5 0.038
A1 Blood Group A (100%) A1p 5.0125 2 0.946
A6 Terminal N-Actyl Galactosamine 5-Acetyl Neuramic Acid (100%) A6p 5.0125 4 0.761
B0 O-GalNAc Core 6 (100%) B0p 0.379677 1 0.417
C0 Blood Group H (93%) C0p 7.75429 5 1.000
D0 Terminal Mannose (96%) D0p 10 3 0.997
E0 E0p 1.89675 22 0.000
0 Non-Binders (100%) 8.22797 16 NA
A4 Terminal N-Actyl Galactosamine (92%) A4p NA NA 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 0.000e+00 1449.8 4.155 {<3f4f6f>GalNAcA1-3<4f6f>GalB1-<3or4><2f6f><GlcorGlcNAc>B}
A2 A2p A2Full 2.310e-01 23279.1 6.787 {<3f4f6f>GalNAcA}
A3 A3p A3Full 3.690e-01 7725.4 2.106 {<3f4f6f>GalNAcB1-4<3f6f>GlcNAcB1-2<3f4f6f>ManA1-6(<3f4f6f>GalNAcB1-4<3f6f>GlcNAcB1-2<3f4f6f>ManA1-3)<2f4f>ManB1-4<3f6f>GlcNAcB1-4<1f3f6f>GlcNAc?} {Spacer:Asn}
A4 A4p A4Full 7.000e-03 657.1 10.948 {<3f4f6f>GalNAcB1-4(<2f3f4f>FucA1-3)<1f6f>GlcNAcB} {Spacer:NCCO}
A5 A5p A5Full 2.740e-01 41674.5 2.982 {<3f4f6f>GalNAcB1-4<6f>GlcNAc?}
A6 A6p A6Full 1.000e-03 1825.3 7.850 {<3f4f6f>GalNAcB1-4<2f6f>GalB}
A0 A0p A0Full 2.380e-01 20461.3 3.051 {<3f4f6f>GalNAc?}
B0 B0p B0Full 3.810e-01 28477.7 2.767 {<2f3f4f6f>GalB1-4<3f6f>GlcNAcB1-6<1f3f4f>GalNAcA} {Spacer:NCCCO}
C0 C0p C0Full 9.448e+03 65534.2 0.237 {<2f3f4f>FucA1-2<3f4f6f>GalB1-3<4f6f>GalNAc?}
D0 D0p D0Full 4.131e+05 17179.2 0.058 {<2f3f4f6f>ManA1-6(<3f4f6f>ManA1-3)<2f4f>ManB}
E0 E0p E0Full 0.000e+00 2672.4 4.850 {<4f5f>Any?1-<2or3or4>(6S)<GalorGlcorGlcNAc>B}

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