Biomedical subjects

Mark van der Laan

Publications and source records attributed to Mark van der Laan.

3 recordsLinked to original sources

PubMed2003

Exploratory and confirmatory gene expression profiling of mac1Delta.

Exploratory outlier identification methods and confirmatory gene expression studies showed induction of the iron regulon in Saccharomyces cerevisiae lacking Mac1p, a copper-responsive transcription factor. The Aft1p/Aft2p binding motif was the most discriminating motif between up- and down-regulated genes, and we identified new genes potentially regulated by Aft1p/Aft2p. In addition, multiple genes encoding proteins containing Fe-S clusters were down-regulated suggesting metabolic reorganization to conserve iron in mac1Delta. Null mutants of each of the differentially expressed genes were characterized for copper- or iron-related phenotypes. New or additional support for a role in copper and iron homeostasis is provided in this study for the gene products of AKR1, MRS4, PCA1, SSU1, TIS11, YBR047W, YHL035C, YHR045W, YLR047C, YLR126C, and YTP1.

Base Sequence↗

PubMed2002

Modeling treatment effects on binary outcomes with grouped-treatment variables and individual covariates.

During evaluation of treatment effects in observational studies, confounding is a constant threat because it is always possible that patients with a better prognosis, not adequately characterized by measured covariates, are chosen for a specific therapy. Ecologic analyses may avoid confounding that would be present in analysis at the individual level because variations in regional or hospital practice may be unrelated to prognosis. The authors used simulated data with an excluded confounder to evaluate the reliability and limitations of the grouped-treatment approach, a method of incorporating an ecologic measure of treatment assignment into an individual-level multivariable model, similar to the instrumental variable approach. Estimates based on the grouped-treatment approach were closer to the true value than those of standard individual-level multivariable analysis in every simulation. Furthermore, confidence intervals based on the grouped-treatment approach achieved approximately their nominal coverage, whereas those based on individual-level analyses did not. The grouped-treatment approach appears to be more reliable than standard individual-level analysis in situations where the grouped-treatment variable is unassociated with the outcome except via the actual treatment assignment and measured covariates.

Confounding Factors, Epidemiologic↗

PubMed2002

Identification of regulatory elements using a feature selection method.

MOTIVATION: Many methods have been described to identify regulatory motifs in the transcription control regions of genes that exhibit similar patterns of gene expression across a variety of experimental conditions. Here we focus on a single experimental condition, and utilize gene expression data to identify sequence motifs associated with genes that are activated under this experimental condition. We use a linear model with two-way interactions to model gene expression as a function of sequence features (words) present in presumptive transcription control regions. The most relevant features are selected by a feature selection method called stepwise selection with monte carlo cross validation. We apply this method to a publicly available dataset of the yeast Saccharomyces cerevisiae, focussing on the 800 basepairs immediately upstream of each gene's translation start site (the upstream control region (UCR)). RESULTS: We successfully identify regulatory motifs that are known to be active under the experimental conditions analyzed, and find additional significant sequences that may represent novel regulatory motifs. We also discuss a complementary method that utilizes gene expression data from a single microarray experiment and allows averaging over variety of experimental conditions as an alternative to motif finding methods that act on clusters of co-expressed genes. AVAILABILITY: The software is available upon request from the first author or may be downloaded from http://www.stat.berkeley.edu/~sunduz. CONTACT: keles@stat.berkeley.edu

Amino Acid Motifs↗