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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.
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Theoretical Biology and Medical Modelling

ISSN: 1742-4682