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Table 2 Alternative spliced genes inferred by applying Hu's method to our dataset: Comparison of normal cerebellum with medulloblastoma samples

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

Affy Probe Set ID Gene Symbol Number of Affymetrix Probes in the Predicted Pseudo-exon Nucleotide Positions of Predicted Pseudo-exon in the Gene Description of the Genes
X51362_s_at DRD2 2 (2541–2574) dopamine receptor D2
M15517_cds5_at TTR 3 (155–197) transthyretin (prealbumin, amyloidosis type I)
Y10141_s_at SLC6A3 2 (96–125) solute carrier family 6 (neurotransmitter transporter, dopamine), member 3
Z14982_rna1_at PSMB8 2 (820–850) proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)
X69654_at RPS26 2 (9–35) ribosomal protein S26
U63842_at NEUROG1 2 (834–891) neurogenin 1
M97815_at CRABP2 2 (524–554) cellular retinoic acid binding protein 2
D00017_at ANXA2 2 (1229–1265) annexin A2
U13021_s_at CASP2 3 (844–913) caspase 2, apoptosis-related cysteine protease (neural precursor cell expressed, developmentally down-regulated 2)
U30999_at ALCAM 2 (373–403) activated leukocyte cell adhesion molecule
X04828_at GNAI2 3 (1668–1701) guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2
U14971_at RPS9 2 (319–373) ribosomal protein S9
U79299_at OLFM1 2 (1342–1372) olfactomedin 1
L20298_at CBFB 2 (2298–2334) core-binding factor, beta subunit
X93017_at SLC8A3 2 (1725–1821) solute carrier family 8 (sodium-calcium exchanger), member 3
M17886_at RPLP1 2 (127–163) ribosomal protein, large, P1
D16480_at HADHA 2 (2335–2365) hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit
D38305_at TOB1 2 (707–749) transducer of ERBB2, 1
U32519_at G3BP 2 (1534–1564) Ras-GTPase-activating protein SH3-domain-binding protein
U07919_at ALDH1A3 3 (3363–3411) aldehyde dehydrogenase 1 family, member A3
U29953_rna1_at SERPINF1 2 (1288–1324) serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1
D55716_at MCM7 2 (2288–2396) MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)
J05448_at POLR2C 2 (1575–1605) polymerase (RNA) II (DNA directed) polypeptide C, 33 kDa
U46570_at TTC1 2 (1226–1262) tetratricopeptide repeat domain 1
D87119_at TRB2 2 (4022–4136) tribbles homolog 2
X69910_at CKAP4 2 (2543–2573) cytoskeleton-associated protein 4
U50078_at HERC1 2 (14885–14915) hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1
J04164_at IFITM1 2 (798–828) interferon induced transmembrane protein 1 (9–27)
AFFX-HUMRGE/M10098_3_at N/A 2 (1562–1613) N/A
HG2788-HT2896_at N/A 2 (N/A-N/A) N/A
HG2994-HT4850_s_at N/A 2 (N/A-N/A) N/A
  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.