rSRL_CFG_1
Automated Analysis report for rSRL_CFG_1 evaluated at 2 ug/mL
List of Primary rSRL_CFG_1 Motifs
| Primary Motif ID | Primary Motif Minimal Structure | Primary Motif Complete Structure | Relative Binding | Number of Glycans |
|---|---|---|---|---|
| A |  |
 |
0.86 | 10 |
| B |  |
 |
1.00 | 5 |
| C |  |
 |
0.16 | 48 |
| D |  |
 |
0.14 | 50 |
| E |  |
 |
0.12 | 29 |
| F |  |
 |
0.00 | 23 |
| 0 | 0.00 | 443 |
Minimal and complete motif definitions match the same set of glycans defined in the array. Components found in the complete motif but excluded in the minimal motif are not tested by the array. Monosaccharide identities and subsitution intolerance may or may not have been tested by the array, they are retained from the complete motif for readability.
Boxplot of Primary Motifs
List of Fine-Specificity rSRL_CFG_1 Motifs
| Motif ID | Nearest Common Name (Accuracy%**) | Motif Graphic Structure | Relative Binding | Number of Glycans | P-Value*** |
|---|---|---|---|---|---|
| A0 | Terminal N-Glycan N-Acetyl Glucosamine (99%) | |
0.86 | 10 | <0.001 |
| B0 | Terminal alpha N-Acetyl Glucosamine (99%) | |
1.00 | 5 | <0.001 |
| C0* | Terminal beta N-Acetyl Glucosamine (93%) | |
0.18 | 41 | <0.001 |
| C1 | Terminal beta N-Acetyl Glucosamine O-GalNAc (98%) |  |
0.00 | 7 | 1.000 |
| D0* | Terminal alpha N-Acetyl Glucosamine (99%) | |
0.56 | 4 | <0.001 |
| D4* | Terminal N-Glycan N-Acetyl Glucosamine (98%) |  |
0.37 | 4 | <0.001 |
| D7 | alpha-Fucose Terminal N-Glycan N-Acetyl Glucosamine (99%) |  |
0.36 | 4 | <0.001 |
| D2 |  |
0.00 | 16 | 1.000 | |
| D6 | GlcNAc Base 6’ Sulfated Galactose or N-AcetylGalactosamine (98%) |  |
0.00 | 4 | 1.000 |
| D3 | Bisecting N-Glycan (97%) |  |
0.00 | 5 | 1.000 |
| D5 | Bisecting N-Glycan (97%) |  |
0.00 | 3 | 1.000 |
| D1 | O-GlcNAc Core Sialyl Dimer (99%) |  |
0.00 | 10 | 1.000 |
| E0* | O-GalNAc Core 1 (98%) | |
0.12 | 22 | <0.001 |
| E1 | O-GalNAc Core 2 (99%) |  |
0.10 | 7 | 0.010 |
| F0 | Blood Group A (100%) | |
0.00 | 23 | 1.000 |
| 0 | Non-Binders (100%) | 0.00 | 443 | NA |
Key:
See Symbol Nomenclature for Glycans (SNFG) for complete key: https://www.ncbi.nlm.nih.gov/glycans/snfg.html
*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.
Boxplot of Fine-Specificity Motifs
Figure 1. Glycan binding grouped by motif and motif family. Individual glycans are given as points on the plot.
Motif Intensity Map
Figure 2. 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.
Motif Family Membership Map
*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 3. 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.
Detailed Model Breakdown
Motif Glycan Examples:
| Motif ID | Motif Minimal Graphic | Motif Complete Graphic | Highest Glycan | Moderate Glycan | Lowest Glycan |
|---|---|---|---|---|---|
| A0 | |
|
 |
 |
 |
| B0 | |
|
 |
 |
 |
| C1 | |
 |
 |
 |
 |
| C0 | |
|
 |
 |
 |
| D1 | |
 |
 |
 |
 |
| D2 | |
 |
 |
 |
 |
| D3 | |
 |
 |
 |
 |
| D4 | |
 |
 |
 |
 |
| D5 | |
 |
 |
 |
 |
| D6 | |
 |
 |
 |
 |
| D7 | |
 |
 |
 |
 |
| D0 | |
|
 |
 |
 |
| E1 | |
 |
 |
 |
 |
| E0 | |
|
 |
 |
 |
| F0 | |
|
 |
 |
 |
| 0 |  |
 |
 |
Key:
All Concentration Plots:
Figure 4. Boxplots of glycan binding grouped by motif for each dataset in the model. Motifs are listed in ascending average binding intensity (for the selected concentration) and colored by family.
Model Structure:
*Motif matches the remaining glycans not matched by earlier motifs in the model.
Figure 5. 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.
Curve Fitting:
Figure 6. Logistic curves fit to average motif 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. Nonbinding motifs are excluded from the plot.
Motif Curve Parameter Scatterplots
Figure 7. Scatterplots of motif curve parameters. Plotting the asymptote of the curve and the slope of the curve over the log 10 Kd of the motif allows for critical assesment and comparison of motif curves. Note that the apparent Kd of the motif is the concentration at which the curve is half of the asymptote. A standard logistic slope of 1 is marked in a dashed line for reference. Nonbinding motifs are excluded from the plot. The highest affinity motifs which show the best concentration dependent response are in the top left of the top plot. Curves which have very low slopes may also indicate nonspecific binding while higher slopes may indicate higher order binding.
| Motif ID | Motif Graphic Structure | Estimated Kd (ug/mL) | Curve Asymptote | Hill Slope |
|---|---|---|---|---|
| A0 | |
5.871 | 19438 | 0.613 |
| B0 | |
8.351 | 23838 | 0.521 |
| C1 | |
290.846 | 65535 | 1.591 |
| C0* | |
460.867 | 65535 | 0.703 |
| D4* | |
127.537 | 29211 | 0.536 |
| D7 | |
20.103 | 14478 | 0.633 |
| D0* | |
179.941 | 45393 | 0.503 |
| E1 | |
193.257 | 47955 | 0.893 |
| E0* | |
74.395 | 18227 | 0.821 |
| F0 | |
181.515 | 32537 | 4.702 |
Motif Text Structures:
| Motif ID | Motif Graphic | Motif Text |
|---|---|---|
| A0 | |
<3f4f6f>GlcNAcB1-2<3f4f6f>ManA1-<3or6><2f4f>ManB |
| B0 | |
<3f4f6f>GlcNAcA1-4<2f3f6f>GalB1-4<3f6f>GlcNAcB |
| C1 | |
<3f4f6f>GlcNAcB1-<3or4><1f2f><FucorGalNAcorGlcNAc>A |
| C0* | |
<3f4f6f>GlcNAcB1-<3or4or6><2f><FucorGalorGalNAcorGlcNAc>? |
| D1 | |
<2f4f>GalB1-4<3f6f>GlcNAcA |
| D2 | |
<4f><GlcNAcorManorNeu5Ac>?<1or2>-<4or6><3f>GlcNAcB1-4<1f3f6f>GlcNAcA |
| D3 | |
<2f4f6f>GalB1-<3or4><6f>GlcNAcB1-2<3f4f>ManA1-6(<3f4f6f>GlcNAcB1-4)<2f>ManB1-4<3f6f>GlcNAcB1-4<1f3f6f>GlcNAcA |
| D4* | |
<3f>GlcNAcB1-4<1f3f6f>GlcNAcA |
| D5 | |
<2f3f4f6f>GalB1-4<3f6f>GlcNAcB1-2<3f4f>ManA1-6<2f>ManB1-4<3f6f>GlcNAcB1-4(<2f3f4f>FucA1-6)<1f3f>GlcNAcA |
| D6 | |
GalNAcB1-4<1f3f>GlcNAcA |
| D7 | |
<2f><FucorMan>?1-<2or4><6f><GalorGlcNAc>B1-4<1f3f>GlcNAcA |
| D0* | |
<3f>GlcNAcA |
| E1 | |
<2f4f>GalB1-4<3f6f>GlcNAcB1-6(<2f3f4f6f>GalB1-3)<1f4f>GalNAcA |
| E0* | |
<4f6f>GalB1-3<1f4f>GalNAcA |
| F0 | |
<3f4f6f>GalNAcA1-3<4f6f>GalB |
| 0 | Non-Binders |
Key: