Biomedical subjects

Daniel Yekutieli

Publications and source records attributed to Daniel Yekutieli.

5 recordsLinked to original sources

PubMed2006

SKY analysis of childhood neural tumors and cell lines demonstrates a susceptibility of aberrant chromosomes to further rearrangements.

Malignant solid tumors are commonly characterized by a large number of complex structural and numerical chromosomal alterations, which often reflect the level of genomic instability and can be associated with disease progression. The aim of this study was to evaluate whether chromosomes that harbor primary aberrations have a higher susceptibility to accumulate further alterations. We used spectral karyotyping (SKY), to compare the individual chromosomal instability of two chromosome types: chromosomes that have a primary aberration and chromosomes without an aberration, in 13 primary childhood neural tumors and seven cell lines. We found that chromosomes that contain a primary aberration are significantly (p-value<0.001) more likely to gain further structural rearrangements or to undergo numerical changes (22.6%, 36 of 159 chromosomes) than chromosomes with no initial aberration (4.9%, 54 of 1099 chromosomes). These results are highly suggestive that aberrant chromosomes in solid tumors have a higher susceptibility to accumulate further rearrangements than "normal" chromosomes.

Aneuploidy↗

PubMed2006

Cluster-based analysis of FMRI data.

We propose a method for the statistical analysis of fMRI data that tests cluster units rather than voxel units for activation. The advantages of this analysis over previous ones are both conceptual and statistical. Recognizing that the fundamental units of interest are the spatially contiguous clusters of voxels that are activated together, we set out to approximate these cluster units from the data by a clustering algorithm especially tailored for fMRI data. Testing the cluster units has a two-fold statistical advantage over testing each voxel separately: the signal to noise ratio within the unit tested is higher, and the number of hypotheses tests compared is smaller. We suggest controlling FDR on clusters, i.e., the proportion of clusters rejected erroneously out of all clusters rejected and explain the meaning of controlling this error rate. We introduce the powerful adaptive procedure to control the FDR on clusters. We apply our cluster-based analysis (CBA) to both an event-related and a block design fMRI vision experiment and demonstrate its increased power over voxel-by-voxel analysis in these examples as well as in simulations.

Algorithms↗

PubMed2005

Quantitative trait Loci analysis using the false discovery rate.

False discovery rate control has become an essential tool in any study that has a very large multiplicity problem. False discovery rate-controlling procedures have also been found to be very effective in QTL analysis, ensuring reproducible results with few falsely discovered linkages and offering increased power to discover QTL, although their acceptance has been slower than in microarray analysis, for example. The reason is partly because the methodological aspects of applying the false discovery rate to QTL mapping are not well developed. Our aim in this work is to lay a solid foundation for the use of the false discovery rate in QTL mapping. We review the false discovery rate criterion, the appropriate interpretation of the FDR, and alternative formulations of the FDR that appeared in the statistical and genetics literature. We discuss important features of the FDR approach, some stemming from new developments in FDR theory and methodology, which deem it especially useful in linkage analysis. We review false discovery rate-controlling procedures--the BH, the resampling procedure, and the adaptive two-stage procedure-and discuss the validity of these procedures in single- and multiple-trait QTL mapping. Finally we argue that the control of the false discovery rate has an important role in suggesting, indicating the significance of, and confirming QTL and present guidelines for its use.

Chromosome Mapping↗

PubMed2005

Prior exercise training improves the outcome of acute myocardial infarction in the rat. Heart structure, function, and gene expression.

OBJECTIVES: The aim of this research was to investigate the structural, functional, and molecular features of the remodeling heart in prior swim-trained infarcted rats. BACKGROUND: Physical exercise training is a known protective factor against cardiovascular morbidity and mortality. The structural and molecular aspects underlying this protection in the remodeling heart have not been investigated. METHODS: After seven weeks of swimming exercise training, rats underwent surgical ligation of the left coronary artery followed by a four-week sedentary period. Untrained control rats underwent the same surgical protocol. Left ventricular function was assessed by echocardiography four weeks after infarction, and hearts were sampled for histological and molecular analysis. Ribonucleic acid from the surviving left ventricle was analyzed by complementary deoxyribonucleic acid arrays followed by Northern blotting or quantitative reverse transcription polymerase chain reaction of selected messenger ribonucleic acids (mRNAs). RESULTS: Scar area was 1.6-fold smaller (p = 0.0002), arteriolar density was 1.7-fold higher (p = 0.0002), and left ventricular shortening fraction was 1.9-fold higher (p = 0.003) in the exercise-trained compared with sedentary hearts. Eleven genes whose expression level varied by at least +/-1.5-fold distinguished the prior exercised rats from their sedentary counterparts. Compared with sedentary, the exercised hearts displayed 9- and 2.4-times lower levels of atrial natriuretic peptide and aldolase mRNA (p = 0.03 and 0.04, respectively), and a 2.7- and 1.9-fold higher abundance of cytochrome c-oxidase and fatty acid binding protein, respectively (p < 0.03, each). CONCLUSIONS: Swimming exercise training before acute myocardial infarction reduces scar size, increases arteriole density, and manifests adaptation of stress- and energy-metabolism-related genes that may contribute to the improved heart function observed during remodeling.

Adenosine Triphosphatases↗

PubMed2003

Identifying differentially expressed genes using false discovery rate controlling procedures.

MOTIVATION: DNA microarrays have recently been used for the purpose of monitoring expression levels of thousands of genes simultaneously and identifying those genes that are differentially expressed. The probability that a false identification (type I error) is committed can increase sharply when the number of tested genes gets large. Correlation between the test statistics attributed to gene co-regulation and dependency in the measurement errors of the gene expression levels further complicates the problem. In this paper we address this very large multiplicity problem by adopting the false discovery rate (FDR) controlling approach. In order to address the dependency problem, we present three resampling-based FDR controlling procedures, that account for the test statistics distribution, and compare their performance to that of the naïve application of the linear step-up procedure in Benjamini and Hochberg (1995). The procedures are studied using simulated microarray data, and their performance is examined relative to their ease of implementation. RESULTS: Comparative simulation analysis shows that all four FDR controlling procedures control the FDR at the desired level, and retain substantially more power then the family-wise error rate controlling procedures. In terms of power, using resampling of the marginal distribution of each test statistics substantially improves the performance over the naïve one. The highest power is achieved, at the expense of a more sophisticated algorithm, by the resampling-based procedures that resample the joint distribution of the test statistics and estimate the level of FDR control. AVAILABILITY: An R program that adjusts p-values using FDR controlling procedures is freely available over the Internet at www.math.tau.ac.il/~ybenja.

Algorithms↗