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.
Figure 2. Boxplots of glycans grouped by primary motif. Individual points are glycans. Mouseover to see glycan structures.
| A |
 |
1.00 |
35 |
| 0 |
|
0.00 |
573 |
Figure 2. Boxplots of glycans grouped by primary motif. Individual points are glycans. Mouseover to see glycan structures.
| A |
|
1.00 |
35 |
| 0 |
|
0.00 |
573 |
Figure 2. Boxplots of glycans grouped by primary motif. Individual points are glycans. Mouseover to see glycan structures.
| A |
|
65.1603 |
33 |
*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.
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.
*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.
*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.
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).
| | | | | |
|---|
| 473 | A0 | 18.67169 | 1296.088 | 1 | |
| 420 | A0 | 20.55854 | 1550.097 | 1 | |
| 427 | A0 | 25.05765 | 2670.524 | 1 | |
| 365 | A0 | 25.56075 | 2316.506 | 1 | |
| 426 | A0 | 28.89764 | 3207.297 | 1 | |
| 352 | A0 | 29.25016 | 4609.171 | 1 | |
| 578 | A4 | 35.61309 | 4566.276 | 1 | |
| 454 | A0 | 36.39045 | 2111.386 | 1 | |
| 472 | A0 | 38.04027 | 4299.896 | 1 | |
| 353 | A0 | 39.45059 | 7253.337 | 1 | |
| A1 |
 |
 |
102.61 |
4976 |
1 |
{KVA{<2f4f6f>GalB1-<3or4><6f>GlcNAcB1-3<2f4f6f>GalB1-4<3f6f>GlcNAcB1-6(<2f4f6f>GalB1-<3or4><6f>GlcNAcB1-3<2f4f6f>GalB1-4<3f6f>GlcNAcB1-2)<3f4f>ManA1-6(<2f4f6f>GalB1-<3or4><6f>GlcNAcB1-3<2f4f6f>GalB1-4<3f6f>GlcNAcB1-2<3f4f6f>ManA1-3)<2f4f>ManB1-4<3f6f>GlcNAcB1-4(<2f3f4f>FucA1-6)<3f>GlcNAcB}NK^T}
{Spacer:KVANKT} |
| A2 |
 |
 |
55.29 |
8337 |
1 |
{A{<3f6f>GlcNAcB1-6(<3f6f>GlcNAcB1-2)<3f4f>ManA1-6(<3f6f>GlcNAcB1-2<3f4f6f>ManA1-3)<2f4f>ManB1-4<3f6f>GlcNAcB1-4(<2f3f4f>FucA1-6)<3f>GlcNAcB}NK^T}
{Spacer:KVANKT} |
| A3 |
 |
 |
86.91 |
20215 |
1 |
{KVA{<4f6f8f>Neu5AcA2-6<2f3f4f>GalB1-4<3f6f>GlcNAcB1-2<3f4f6f>ManA1-6(<4f6f8f>Neu5AcA2-6<2f3f4f>GalB1-4<3f6f>GlcNAcB1-2<3f4f6f>ManA1-3)<2f4f>ManB1-4<3f6f>GlcNAcB1-4(<2f3f4f>FucA1-6)<3f>GlcNAcB}NK^T}
{Spacer:KVANKT} |
| A4 |
 |
 |
80.22 |
9766 |
1 |
{KVA{<3f6f8f><GlcNAcorNeu5Ac>?<1or2>-<3or6><2f4f>GalB1-4<3f6f>GlcNAcB1-2<3f4f6f>ManA1-6(<3f6f8f><GlcNAcorNeu5Ac>?<1or2>-<3or6><2f4f>GalB1-4<3f6f>GlcNAcB1-2<3f4f6f>ManA1-3)<2f4f>ManB1-4<3f6f>GlcNAcB1-4(<2f3f4f>FucA1-6)<3f>GlcNAcB}NK^T}
{Spacer:KVANKT} |
| A0 |
|
 |
38.96 |
4027 |
1 |
{^x{<3f4f6f>ManA1-3(<3f4f>ManA1-6)<2f4f>ManB1-4<3f6f>GlcNAcB1-4(<2f3f4f>FucA1-6)<3f>GlcNAcB}N} |
