A statistical method for predicting splice variants between two groups of samples using GeneChip ® expression array data

Table 1 Alternative spliced genes selected by our method: Comparison of non-metastatic medulloblastomas with metastatic medulloblastomas

Affymetrix Probe Set ID	Gene Symbol	Number of Affymetrix Probes in the Predicted Pseudo-exon	Nucleotide Positions of Predicted Pseudo-exon in the Gene	Mean Difference	Standard Error	Z-score	Description of the Genes
M81882_at	GAD2	4	(2135–2285)	-1.28	0.20	-6.45	glutamate decarboxylase 2 (pancreatic islets and brain, 65 kDa)
M13955_at	KRT7	5	(1402–1474)	-0.63	0.12	-5.23	keratin 7
U17327_at	NOS1	7	(6805–7003)	-0.66	0.13	-5.19	nitric oxide synthase 1 (neuronal)
X14329_at	CPN1	4	(1569–1665)	-0.62	0.12	-5.18	carboxypeptidase N, polypeptide 1, 50 kD
M89470_s_at	PAX2	6	(2855–2972)	-0.92	0.19	-4.91	paired box gene 2
L14542_at	KLRC3	5	(916–1006)	-1.18	0.24	-4.91	killer cell lectin-like receptor subfamily C, member 3
X76648_at	GLRX	3	(704–776)	-1.35	0.28	-4.86	glutaredoxin (thioltransferase)
U82987_at	BBC3	3	(1578–1638)	2.25	0.32	6.98	BCL2 binding component 3
U01102_at	SCGB1A1	2	(409–439)	1.42	0.25	5.62	secretoglobin, family 1A, member 1 (uteroglobin)
M28219_at	LDLR	15	(67–277)	0.77	0.14	5.42	low density lipoprotein receptor (familial hypercholesterolemia)
X68194_at	SYPL	5	(1915–2089)	1.67	0.31	5.42	synaptophysin-like protein
U85267_at	DSCR1	10	(64–169)	1.20	0.24	5.08	Down syndrome critical region gene 1
L36051_at	THPO	6	(1647–1809)	1.05	0.21	4.96	thrombopoietin (myeloproliferative leukemia virus oncogene ligand, megakaryocyte growth and development factor)

Number of Affymetrix Probes in the Predicted Pseudo-exon: number of probes that are contained in a predicted alternatively spliced pseudo-exon. Nucleotide Positions of Predicted Pseudo-exon in the Gene: nucleotide positions of the pseudo-exon from the beginning of the gene it resides. Mean difference: Mean difference of the expression values between the two tissue types being compared for each predicted pseudo-exon in the t-test in STEP 2. Standard Error: the standard error calculated in the same t-test. Z-score: the ratio of mean difference over standard error (noise), a measure of significance of the difference between the two tissues being compared. The sign of the Z-scores indicate direction of the difference. A negative Z-score means a lower expression in metastatic medulloblastomas than in non-metastatic medulloblastomas, and vice-versa for a positive Z-score.