Biomedical subjects

Xiaoyan Leng

Publications and source records attributed to Xiaoyan Leng.

3 recordsLinked to original sources

PubMed2006

Time ordering of gene coexpression.

Temporal microarray gene expression profiles allow characterization of gene function through time dynamics of gene coexpression within the same genetic pathway. In this paper, we define and estimate a global time shift characteristic for each gene via least squares, inferred from pairwise curve alignments. These time shift characteristics of individual genes reflect a time ordering that is derived from ob- served temporal gene expression profiles. Once these time shift characteristics are obtained for each gene, they can be entered into further analyses, such as clustering. We illustrate the proposed methodology using Drosophila embryonic development and yeast cell-cycle gene expression profiles, as well as simulations. Feasibility is demonstrated through the successful recovery of time ordering. Estimated time shifts for Drosophila maternal and zygotic genes provide excellent discrimination between these two categories and confirm known genetic pathways through the time order of gene expression. The application to yeast cell-cycle data establishes a natural time order of genes that is in line with cell-cycle phases. The method does not require periodicity of gene expression profiles. Asymptotic justifications are also provided.

Animals↗

PubMed2005

Classification using functional data analysis for temporal gene expression data.

MOTIVATION: Temporal gene expression profiles provide an important characterization of gene function, as biological systems are predominantly developmental and dynamic. We propose a method of classifying collections of temporal gene expression curves in which individual expression profiles are modeled as independent realizations of a stochastic process. The method uses a recently developed functional logistic regression tool based on functional principal components, aimed at classifying gene expression curves into known gene groups. The number of eigenfunctions in the classifier can be chosen by leave-one-out cross-validation with the aim of minimizing the classification error. RESULTS: We demonstrate that this methodology provides low-error-rate classification for both yeast cell-cycle gene expression profiles and Dictyostelium cell-type specific gene expression patterns. It also works well in simulations. We compare our functional principal components approach with a B-spline implementation of functional discriminant analysis for the yeast cell-cycle data and simulations. This indicates comparative advantages of our approach which uses fewer eigenfunctions/base functions. The proposed methodology is promising for the analysis of temporal gene expression data and beyond. AVAILABILITY: MATLAB programs are available upon request.

Algorithms↗

PubMed2004

The influence of patient- and facility-specific factors on nutritional status and survival in hemodialysis.

BACKGROUND: Parameters of nutritional status, including serum albumin, serum creatinine, and body mass index (BMI), are powerful predictors of mortality and hospitalization in patients with end stage renal disease (ESRD). Patient-specific characteristics and facility-related practice patterns modify certain parameters of nutritional status. We aimed to determine whether patient and facility characteristics modify the risk profiles associated with malnutrition in hemodialysis patients. METHODS: We analyzed data on 5,234 prevalent hemodialysis patients from the Dialysis Morbidity and Mortality Study (DMMS) Wave 1 for whom information on demographic, clinical, nutritional, and facility-related characteristics were available. We evaluated the associations among facility characteristics and serum albumin, serum creatinine, and BMI, adjusting for the effects of age, sex, race/ethnicity, diabetes, and dialysis vintage. We determined correlates of mortality and hospitalization, focusing on nutritional parameters, facility effects, and the interactions among patient-specific and facility-specific characteristics, albumin, creatinine, and BMI. RESULTS: Serum albumin was lower with older age, diabetes, nonblack race, and hemodialysis using a catheter. Serum albumin was higher with annual vascular access surveillance, higher BMI among women, higher urea reduction ratio, among patients in whom dialyzers were reprocessed (particularly with bleach), among dialysis units in which water purification was used, and when vascular access blood flow rates were > or =350 mL/min. Overall survival was decreased with lower albumin, creatinine, and BMI. There were interactions among albumin, age, and vintage. Whereas lower serum albumin concentrations consistently were associated with an increased risk of death, the differences were attenuated among older patients and accentuated among patients of longer vintage. CONCLUSION: Some facility-specific factors are associated with nutritional parameters including serum albumin, serum creatinine, and BMI. The associations of nutritional parameters with mortality and hospitalization vary by age, sex, and vintage but not by facility-specific factors, including those associated with the nutritional parameters themselves.

Adult↗