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

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

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)
  1. 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.
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Theoretical Biology and Medical Modelling

ISSN: 1742-4682