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Blood, Vol. 107, Issue 2, 769-776, January 15, 2006
The expression of 70 apoptosis genes in relation to lineage, genetic subtype, cellular drug resistance, and outcome in childhood acute lymphoblastic leukemia
Blood Holleman et al.
107: 769
Supplemental materials for: Holleman et al
Files in this Data Supplement:
- Table S1. Median expression of 118 apoptosis probe sets in different immunophenotypic and genetic ALL subtypes at initial diagnosis (PDF, 23.8 KB) -
The median expression for each individual apoptosis gene is indicated in each subgroup defined by lineage or genetic subtype, i.e. ploidy (- = non-hyperdiploid, + = hyperdiploid), TEL-AML1 status (- = TEL-AML1 negative, + = TEL-AML1 positive), and E2A status (- = E2A germline, + = E2A-rearranged).
- Table S2. Median expression of 118 apoptosis probe sets in drug resistant and drug sensitive patients in B-lineage ALL at initial diagnosis (PDF, 24.3 KB) -
The median expression for each individual apoptosis gene is indicated in each subgroup defined by in vitro sensitivity and resistance to prednisolone (PRED), vincristine (VCR), L-asparaginase (ASP) and daunorubicin (DNR).
- Table S3. Median expression of 118 apoptosis probe sets at initial diagnosis of children with ALL who stayed in continuous complete remission (CCR) or relapsed during or after completion of chemotherapy (PDF, 19.5 KB) -
The median expression for each individual apoptosis probe set is indicated in each subgroup defined by treatment outcome. The ratio between the expression of each individual apoptosis probe set of children with ALL at initial diagnosis who stayed in continuous complete remission (CCR) or relapsed during or after completion of chemotherapy is indicated in the last column.
- Figure S1. Gene plots for different lineage and genetic ALL subtypes (PDF, 74.3 KB) -
The global test compares two or more groups taking into account the association between probe sets as well as their individual effects. The advantage of the global test is that it is applied to the entire set of probe sets under study at the same time, yielding a single overall P-value. One of the outputs of this test is a so-called gene plot. The height of each individual bar in the gene plot reflects the influence of each probe set on the test result of global test P-value [Reference: Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics. 2004;20:93-99].
Illustrated is the influence of each individual probe set on the outcome of the global test for (A) lineage, i.e. T-lineage ALL versus B-lineage ALL, P<0.001 (B) ploidy, i.e. hyperdiploid versus non-hyperdiploid B-lineage ALL, P<0.001 (C) TEL-AML1 status, i.e. TEL-AML1 positive versus TEL-AML1 negative B-lineage AL, P<0.001 and (D) E2A status, i.e. E2A-rearranged versus E2A-germline B-lineage ALL, P<0.001. The gene plot gives a bar and a reference line (black) for each probe set tested. The reference line reflects the expected height of the bar under the null hypothesis that the probe set is not associated with the variable of interest, i.e. lineage and genetic subtypes. Standard deviations of the mean influence are indicated as black stripes within each bar. Probe sets that influence the model by more than two standard deviations compared to the reference line are selected from each gene plot and included in Table 1 of the original manuscript.
- Figure S2. Gene plots for resistance to 4 individual chemotherapeutic agents in B-lineage ALL (PDF, 84.9 KB) -
Illustrated is the influence of each individual probe set on the outcome of the global test for (A) prednisolone resistance, P=0.007 (B) vincristine resistance, P=0.002 (C) L-asparaginase resistance, P<0.001 and (D) daunorubicin resistance, P=0.37. The gene plot gives a bar and a reference line (black) for each probe set tested. See legend Figure 1 for an explanation of the meaning of individual bars and lines within the gene plot.
- Figure S3. Gene plot for disease-free survival (PDF, 27.7 KB) -
Illustrated is the influence of each individual probe set on the outcome of the global test for disease-free survival, i.e. comparing patients in continuous complete remission (CCR) to patients who relapse (P<0.001). The gene plot gives a bar and a reference line (black) for each gene tested. See legend Figure 1 for an explanation of the meaning of individual bars and lines within the gene plot.
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