Table 3.
Integrative sparse k-means clustering results a
|
Description |
Integrative clustering |
||
|---|---|---|---|
| Dura-Cranial | Blood-Cranial | Blood-Dura-Cranial | |
|
Optimal k classes |
3 |
2 |
2 |
| Class 1 (N) |
19 |
27 |
27 |
| Class 2 (N) |
11 |
13 |
13 |
| Class 3 (N) |
10 |
NA |
NA |
|
Optimal tuning parameter |
0.52 |
0.24 |
0.35 |
| N non-zero weighted features (%)
b
|
|
|
|
| Dura |
6358 (53.9%) |
NA |
3158 (26.8%) |
| Blood |
NA |
1120 (9.5%) |
2372 (20.1%) |
| Cranial |
9 (37.5%) |
2 (8.3%) |
5 (20.8%) |
| Maximum weighted feature (weight) |
|
|
|
| Dura |
MUC4 (0.24) |
NA |
LGALS3 (0.34) |
| Blood |
NA |
RABGAP1 (0.33) |
RABGAP1 (0.26) |
| Cranial |
PFA_TOP (0.73) |
BASTOREF (0.99) |
BASTOREF (0.89) |
|
Gap statistic
c
|
0.128 ± 0.034 |
0.302 ± 0.073 |
0.266 ± 0.079 |
| 95% Confidence interval |
0.062-0.194 |
0.158-0.446 |
0.112-0.420 |
| P-value | 7.41E-05 | 2.01E-05 | 3.59E-04 |
Abbreviations: N number, MUC4 mucin 4 cell surface associated, RABGAP1 RAB GTPase activating protein 1, LGALS3 lectin galactoside-binding soluble 3, BASTOREF basion to reference line, PFA_TOP posterior fossa area above the reference line, NA not applicable.
aDura: dura gene expression data, Blood: blood gene expression data, Cranial: PF trait data.
b11804 gene expression probes and/or 24 posterior fossa traits (features) were used as input.
cThe gap statistic ± standard error is presented. Gap statistics with an approximate p-value less than 0.05 are shown in bold.