Abstract:
:In candidate gene association studies, usually several elementary hypotheses are tested simultaneously using one particular set of data. The data normally consist of partly correlated SNP information. Every SNP can be tested for association with the disease, e.g., using the Cochran-Armitage test for trend. To account for the multiplicity of the test situation, different types of multiple testing procedures have been proposed. The question arises whether procedures taking into account the discreteness of the situation show a benefit especially in case of correlated data. We empirically evaluate several different multiple testing procedures via simulation studies using simulated correlated SNP data. We analyze FDR and FWER controlling procedures, special procedures for discrete situations, and the minP-resampling-based procedure. Within the simulation study, we examine a broad range of different gene data scenarios. We show that the main difference in the varying performance of the procedures is due to sample size. In small sample size scenarios,the minP-resampling procedure though controlling the stricter FWER even had more power than the classical FDR controlling procedures. In contrast, FDR controlling procedures led to more rejections in higher sample size scenarios.
journal_name
Stat Appl Genet Mol Biolauthors
Elsäβer A,Victor A,Hommel Gdoi
10.2202/1544-6115.1729subject
Has Abstractpub_date
2011-01-01 00:00:00pages
Article 51issue
1eissn
2194-6302issn
1544-6115journal_volume
10pub_type
杂志文章abstract::The Dirichlet Process (DP) mixture model has become a popular choice for model-based clustering, largely because it allows the number of clusters to be inferred. The sequential updating and greedy search (SUGS) algorithm (Wang & Dunson, 2011) was proposed as a fast method for performing approximate Bayesian inference ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2018-0065
更新日期:2019-12-12 00:00:00
abstract::Polytomous phenotypes arise when a disease has multiple subtypes or when two dichotomous phenotypes are analyzed simultaneously. Few software programs offer the option to analyze such phenotypes in family studies, and none implements conditional polytomous logistic regression for within-family analysis robust to popul...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2016-0035
更新日期:2017-03-01 00:00:00
abstract::Multiple branching trees have been used to model the acquisition of HIV drug resistance mutations, and several different algorithms have been developed to construct the tree set that best describes the data. These algorithms have mainly focused on the structure of the tree set. The focal point of this paper is estimat...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1324
更新日期:2008-01-01 00:00:00
abstract::Reproducibility of disease signatures and clinical biomarkers in multi-omics disease analysis has been a key challenge due to a multitude of factors. The heterogeneity of the limited sample, various biological factors such as environmental confounders, and the inherent experimental and technical noises, compounded wit...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2018-0039
更新日期:2019-05-11 00:00:00
abstract::Making sound proteomic inferences using ELISA microarray assay requires both an accurate prediction of protein concentration and a credible estimate of its error. We present a method using monotonic spline statistical models (MS), penalized constrained least squares fitting (PCLS) and Monte Carlo simulation (MC) to pr...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1364
更新日期:2008-01-01 00:00:00
abstract::In recent years, alignment-free methods have been widely applied in comparing genome sequences, as these methods compute efficiently and provide desirable phylogenetic analysis results. These methods have been successfully combined with hierarchical clustering methods for finding phylogenetic trees. However, it may no...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2018-0045
更新日期:2019-02-15 00:00:00
abstract::Recent analytic and technological breakthroughs have set the stage for genome-wide linkage disequilibrium studies to map disease-susceptibility variants. This paper discusses a probabilistic methodology for making disease-mapping inferences in large-scale case-control genetic studies. The semi-Bayesian approach promot...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1168
更新日期:2005-01-01 00:00:00
abstract::Usually, a pedigree is sampled and included in the sample that is analyzed after following a predefined non-random sampling design comprising several specific procedures. To obtain a pedigree analysis result free from the bias caused by the sampling procedures, a correction is applied to the pedigree likelihood. The s...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1003
更新日期:2003-01-01 00:00:00
abstract::Integrative analysis of copy number and gene expression data can help in understanding the cis and trans effect of copy number aberrations on transcription levels of genes involved in a pathway. To analyse how these copy number mediated gene-gene interactions differ between groups of samples we propose a new method, n...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2017-0058
更新日期:2018-07-31 00:00:00
abstract::We present a weighted-LASSO method to infer the parameters of a first-order vector auto-regressive model that describes time course expression data generated by directed gene-to-gene regulation networks. These networks are assumed to own prior internal structures of connectivity which drive the inference method. This ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1519
更新日期:2010-01-01 00:00:00
abstract::Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established conce...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2017-0038
更新日期:2018-02-17 00:00:00
abstract::In the exploding field of gene expression techniques such as DNA microarrays, there are still few general probabilistic methods for analysis of variance. Linear models and ANOVA are heavily used tools in many other disciplines of scientific research. The usual F-statistic is unsatisfactory for microarray data, which e...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1125
更新日期:2005-01-01 00:00:00
abstract::The problem of finding periodically expressed genes from time course microarray experiments is at the center of numerous efforts to identify the molecular components of biological clocks. We present a new approach to this problem based on the cyclohedron test, which is a rank test inspired by recent advances in algebr...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1286
更新日期:2007-01-01 00:00:00
abstract::Many gene- and pathway-based association tests have been proposed in the literature. Among them, the SKAT is widely used, especially for rare variants association studies. In this paper, we investigate the connection between SKAT and a principal component analysis. This investigation leads to a procedure that encompas...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2016-0061
更新日期:2017-07-26 00:00:00
abstract::High-throughput sequencing techniques are increasingly affordable and produce massive amounts of data. Together with other high-throughput technologies, such as microarrays, there are an enormous amount of resources in databases. The collection of these valuable data has been routine for more than a decade. Despite di...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2014-0093
更新日期:2015-06-01 00:00:00
abstract::Several important syndromes are caused by deleterious germline mutations of individual genes. In both clinical and research applications it is useful to evaluate the probability that an individual carries an inherited genetic variant of these genes, and to predict the risk of disease for that individual, using informa...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1063
更新日期:2004-01-01 00:00:00
abstract::With the increasing availability of experimental data on gene interactions, modeling of gene regulatory pathways has gained special attention. Gradient descent algorithms have been widely used for regression and classification applications. Unfortunately, results obtained after training a model by gradient descent are...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2012-0021
更新日期:2014-02-01 00:00:00
abstract::There has been increasing interest in predicting patients' survival after therapy by investigating gene expression microarray data. In the regression and classification models with high-dimensional genomic data, boosting has been successfully applied to build accurate predictive models and conduct variable selection s...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1550
更新日期:2010-01-01 00:00:00
abstract::We address a potential shortcoming of three probabilistic models for detecting interspecific recombination in DNA sequence alignments: the multiple change-point model (MCP) of Suchard et al. (2003), the dual multiple change-point model (DMCP) of Minin et al. (2005), and the phylogenetic factorial hidden Markov model (...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1399
更新日期:2008-01-01 00:00:00
abstract::The genetic control of a complex trait can be studied by testing and mapping the genotypes of the underlying quantitative trait loci (QTLs) through their associations with observable marker genotypes. All existing statistical methods for QTL mapping assume an equilibrium population, allowing marker-QTL associations to...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1578
更新日期:2010-01-01 00:00:00
abstract::Output from analysis of a high-throughput 'omics' experiment very often is a ranked list. One commonly encountered example is a ranked list of differentially expressed genes from a gene expression experiment, with a length of many hundreds of genes. There are numerous situations where interest is in the comparison of ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2016-0036
更新日期:2017-03-01 00:00:00
abstract::Multi-color optical mapping is a new technique being developed to obtain detailed physical maps (indicating relative positions of various recognition sites) of DNA molecules. We consider a study design in which the data consist of noisy observations of multiple copies of a DNA molecule marked with colors at recognitio...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1266
更新日期:2007-01-01 00:00:00
abstract::Germline mosaicism is a genetic condition in which some germ cells of an individual contain a mutation. This condition violates the assumptions underlying classic genetic analysis and may lead to failure of such analysis. In this work we extend the statistical model used for genetic linkage analysis in order to incorp...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1709
更新日期:2011-10-04 00:00:00
abstract::We are concerned with statistical inference for 2 × C × K contingency tables in the context of genetic case-control association studies. Multivariate methods based on asymptotic Gaussianity of vectors of test statistics require information about the asymptotic correlation structure among these test statistics under th...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2015-0024
更新日期:2015-11-01 00:00:00
abstract::In this paper, we explore the use of M-quantile regression and M-quantile coefficients to detect statistical differences between temporal curves that belong to different experimental conditions. In particular, we consider the application of temporal gene expression data. Here, the aim is to detect genes whose temporal...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1452
更新日期:2009-01-01 00:00:00
abstract::In this study, we propose a novel statistical framework for detecting progressive changes in molecular traits as response to a pathogenic stimulus. In particular, we propose to employ Bayesian hierarchical models to analyse changes in mean level, variance and correlation of metabolic traits in relation to covariates. ...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2013-0041
更新日期:2014-04-01 00:00:00
abstract::Accurately measuring epigenetic marks such as 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level, requires combining data from DNA processing methods including traditional (BS), oxidative (oxBS) or Tet-Assisted (TAB) bisulfite conversion. We introduce the R package MLML2R, which...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2018-0031
更新日期:2019-01-17 00:00:00
abstract::In cellular biology, node-and-edge graph or "network" data collection often uses bait-prey technologies such as co-immunoprecipitation (CoIP). Bait-prey technologies assay relationships or "interactions" between protein pairs, with CoIP specifically measuring protein complex co-membership. Analyses of CoIP data freque...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.1515/sagmb-2015-0007
更新日期:2015-08-01 00:00:00
abstract::Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a large number of genes; furthermore, the noise level of array experiments is rather high in relation to the available numb...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1132
更新日期:2005-01-01 00:00:00
abstract::The approach adopted involved two-stages. First the 11205 measurements in the mass spectrometry data were reduced to 14 scores by a principal component analysis of the centered but otherwise untreated and unscaled data matrix. Then a linear classifier was derived by linear discriminant analysis using these 14 scores a...
journal_title:Statistical applications in genetics and molecular biology
pub_type: 杂志文章
doi:10.2202/1544-6115.1350
更新日期:2008-01-01 00:00:00