Table 4.
Top 25 Genes Differentially Expressed between AML Patients Who Lived or Died After Treatment
| Gene description | Probe | Z-score | P-value | t-test | W. r.s.3 | Locus | Locus anomalies observed in AML |
| Alpha IV collagen | D17391 | −5.96 | <0.0001 | 1.0000 | 1.0000 | 2q35-q37 | Rearrangement (Berger et al. 1991), ring formation (Whang-Peng et al. 1987) |
| Integrin beta-5 subunit | X53002 | 5.24 | 0.0011 | 1.0000 | 1.0000 | 3 (q22?) | Inversion, translocation (Testoni et al. 1999) |
| Pyrroline-5-carboxylate synthetase | X94453 | 5.00 | 0.0041 | 1.0000 | 1.0000 | 10q24.3 | Translocation in CML (Aguiar et al. 1997), hotspot for translocations in ALL (Kagan et al. 1989; Salvati et al. 1999) |
| Alpha-tubulin | X01703 | 4.96 | 0.0051 | 1.0000 | 1.0000 | 2q | ?, Rearrangement (Berger et al. 1991), ring formation (Whang-Peng et al. 1987) |
| KIAA0076 | D38548 | −4.84 | 0.0092 | 1.0000 | 1.0000 | 6 (p12-21?) | Rearrangement (Raynaud et al. 1994; Haase et al. 1995) |
| Cockayne syndrome complementation group A | U28413 | 4.74 | 0.0147 | 1.0000 | 1.0000 | 5 (q13?) | 5q11-31 frequently lost in AML (Shipley et al. 1996;Van den Berghe and Michaux 1997) |
| Set | M93651 | 4.73 | 0.0158 | 1.0000 | 1.0000 | 9q34 | Translocation, may create Set-Can fusion (von Lindern et al. 1992) |
| KIAA0172 | D79994 | −4.63 | 0.0254 | 1.0000 | 1.0000 | 9 (p?) | 9p abnormalities are common in leukemia and other cancers (Ragione and Iolascon 1997) |
| Selenophosphate synthetase 2 (SPS2) | U43286 | 4.61 | 0.0285 | 1.0000 | 1.0000 | (16p or 10q)? | Inversions and translocations are common in 16p (Marlton et al. 1995; Mancini et al. 2000), CML/ALL translocations identified in 10q (Kagan et al. 1989; Aguiar et al. 1997; Salvati et al. 1999) |
| Centromere protein E (312kD) | Z15005 | −4.60 | 0.0293 | 1.0000 | 1.0000 | 4q24-q25 | 4q25 translocation in ALL (Nowell et al. 1986) |
| Thioredoxin | X77584 | 4.54 | 0.0392 | 1.0000 | 1.0000 | 9q31 | Loss (Shipley et al. 1996) |
| PIG-B | D42138 | −4.53 | 0.0409 | 1.0000 | 1.0000 | 15q21-q22 | 15q observed deleted or translocated (Gogineni et al. 1997; Grimwade et al. 1997) |
| Survival motor neuron protein SMN | U80017 | 4.32 | 0.1088 | 1.0000 | 1.0000 | 5q13 | 5q11-31 frequently lost in AML (Shipley et al. 1996; Van den Berghe and Michaux 1997) |
| Caspase-8 | X98176 | −4.22 | 0.1755 | 1.0000 | 1.0000 | 2q33-q34 | Duplication in non-Hodgkin's lymphoma (Bajalica-Lagercrantz et al. 1996), ring formation (Whang-Peng et al. 1987) |
| Bullous pemphigoid antigen | M69225 | −4.21 | 0.1795 | 1.0000 | 1.0000 | 6p12-p11 | Rearrangement (Raynaud et al. 1994; Haase et al. 1995) |
| Sp2 transcription factor | D28588 | −4.18 | 0.2020 | 1.0000 | 1.0000 | 17q21.3-q22 | Translocation spot (Melnick et al. 1999), isochromosomes on 17q common (Fioretos et al. 1999) |
| Biglycan | J04599 | −4.17 | 0.2119 | 1.0000 | 1.0000 | Xq28 | Translocation found in AML (Weis et al. 1985), common in ALL (Stern 1996) |
| 26S proteasome-associated pad1 homolog (POH1) | U86782 | 4.16 | 0.2226 | 1.0000 | 1.0000 | 2 (q24-32?) | Duplication in non-Hodgkin's lymphoma (Bajalica-Lagercrantz et al. 1996), ring formation (Whang-Peng et al. 1987) |
| Homeobox-like | L32606 | 4.14 | 0.2427 | 1.0000 | 1.0000 | ? | ? |
| Pre-mRNA splicing factor SRP75 | L14076 | −4.13 | 0.2582 | 1.0000 | 1.0000 | 1 (p32-36?) | 1p32 and 1p36 both involved in translocations (Selypes and Laszlo 1987; Shimizu et al. 2000) |
| Autoantigen PM-SCL | X66113 | −4.12 | 0.2614 | 1.0000 | 1.0000 | 1p36 | Translocation (Shimizu et al. 2000) |
| Bactericidal/permeability-increasing protein | J04739 | 4.09 | 0.3030 | 1.0000 | 1.0000 | 20q11.23-q12 | Deletion (commonly deleted in MDS) (Fracchiolla et al. 1998) |
| HoxA9 | U82759 | 4.04 | 0.3836 | 1.0000 | 1.0000 | 7p15-p14 | Inversion (Stanley et al. 1997) |
| Matrin 3 | M63483 | 4.03 | 0.3940 | 1.0000 | 1.0000 |
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Dataset from Golub et al. (1999).
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↵ P-value computed from Z-score using a modified Bonferroni's correction.
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↵ P-value obtained fromtPvalue for TPO was 0.1105 and the Pvalues for the otehr genes did not change.3 P-value obtained from Wilcoxon rank sum using a modified Bonferroni's correction.
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↵Chromosomal locus determined by survey of NCBI LocusLink (http://www.ncbi.nlm.nih.gov/LocusLink). Purative loci are shown in parentheses.
