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6. Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments

Author

Song Peter XK and Gao Xin

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Numerous nonparametric approaches have been proposed in literature to detect differential gene expression in the setting of two user-defined groups. However, there is a lack of nonparametric procedures to analyze microarray data with multiple factors attributing to the gene expression. Furthermore, incorporating interaction effects in the analysis of microarray data has long been of great interest to biological scientists, little of which has been investigated in the nonparametric framework. Results In this paper, we propose a set of nonparametric tests to detect treatment effects, clinical covariate effects, and interaction effects for multifactorial microarray data. When the distribution of expression data is skewed or heavy-tailed, the rank tests are substantially more powerful than the competing parametric F tests. On the other hand, in the case of light or medium-tailed distributions, the rank tests appear to be marginally less powerful than the parametric competitors. Conclusion The proposed rank tests enable us to detect differential gene expression and establish interaction effects for microarray data with various non-normally distributed expression measurements across genome. In the presence of outliers, they are advantageous alternative approaches to the existing parametric F tests due to the robustness feature.

Published
2005
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7. Transition from Donor Candidates to Live Kidney Donors: The Impact of Race and Undiagnosed Medical Disease States

Author

Norman, Silas P., Song, Peter XK, Hu, Youna, and Ojo, Akinlolu O

Subjects
Adult, Male, Tissue and Organ Procurement, Adolescent, Graft Survival, Age Factors, Middle Aged, Kidney Function Tests, Kidney Transplantation, Article, White People, Black or African American, Survival Rate, Young Adult, Treatment Outcome, Hypertension, Living Donors, Humans, Female, Prospective Studies, Aged, Follow-Up Studies
Abstract

Living kidney donors (LKD) allow for increased access to lifesaving organs for transplantation. There is a relative paucity of African American (AA) live kidney donors. The prevalence of medical disease in LKD candidates has not been well studied. We examined the medical limitations to living kidney donation in a large Midwestern transplant center.A total of 2519 adults (age ≥ 18) evaluated as potential LKD (PD) between January 1, 1996 and June 30, 2006 were prospectively followed until evaluation outcome (completed live donation, medical exclusion from live donation, non-medical exclusion from live donation). Logistic regression was used to examine the effect of age on donor exclusion, and chi-square tests were used to compare the likelihood of donor exclusions between racial and gender groups.Sixty percent of PD were female (n = 1300), and 86% were Caucasian (CA) (n = 1862). Overall, 48.7% of PD who underwent evaluation became LKD. The odds of donation were 52% lower in AA compared to CA (OR 0.48 p0.001). Among PD excluded from donation, the most common medical diagnoses were hypertension (HTN) (24.7%), inadequate creatinine clearance (10.6%) and a positive final crossmatch (10.5%). The rate of PD exclusion for obesity was twofold higher in AA compared to CA (12.8% vs. 5.8%, p0.001).Hypertension in PD is equally significant barrier to living kidney donation in AA and CA whereas obesity is a greater barrier in AA.

Published
2011

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