A Robust Topology-Based Algorithm for Gene Expression Profiling

Table 1

The mean correlation distance between each test sample and the core samples of the classical, mesenchymal, and proneural subtypes of GBM. The sample is predicted to belong to a subtype if its mean correlation distance to the core group is smaller than a predetermined value. The 10 assignments provided by our prediction model agree with the TCGA classification.

Patient; sample	Correlation distance; (Clas/Mes)	Correlation; distance; (Proneural)	Correlation; distance (Classical)	Correlation; distance; (Mesenchymal)	Prediction	TCGA; Assignment
TCGA-02-0015	0.60±0.18	1.46±0.11	1.04±0.23	0.72±0.14
TCGA-02-0021	0.39±0.25	1.78±0.07	0.31±0.13	1.61±0.06	C	C
TCGA-02-0026	1.62±0.17	0.27±0.12	—	—	P	P
TCGA-02-0037	0.56±0.15	1.52±0.08	0.88±0.21	1.03±0.11
TCGA-02-0051	0.57±0.27	1.39±0.13	1.26±0.14	0.28±0.08	M	M
TCGA-02-0058	1.49±0.20	0.45±0.17	—	—
TCGA-02-0074	1.58±0.18	0.25±0.13	—	—	P	P
TCGA-02-0075	0.35±0.19	1.74±0.11	1.23±0.14	0.36±0.11	M	M
TCGA-02-0106	0.38±0.17	1.73±0.08	0.91±0.14	0.56±0.12		M
TCGA-02-0451	0.73±0.24	1.38±0.13	—	—		N
TCGA-06-0168	1.19±0.15	0.87±0.11	—	—
TCGA-06-0171	1.48±0.13	0.47±0.08	—	—		N
TCGA-06-0185	0.84±0.33	1.31±0.17	—	—		N
TCGA-06-0190	0.49±0.25	1.56±0.16	1.54±0.14	0.35±0.10	M	M
TCGA-06-0410	1.41±0.28	0.41±0.15	—	—	P	P
TCGA-06-0413	1.67±0.18	0.17±0.08	—	—	P	P
TCGA-08-0359	1.64±0.14	0.25±0.08	—	—	P	P
TCGA-08-0380	1.09±0.24	0.91±0.19	—	—		N
TCGA-08-0517	1.50±0.17	0.38±0.11	—	—	P	P
TCGA-08-0521	0.56±0.25	1.47±0.15	1.58±0.09	0.38±0.13