A Bayesian Hierarchical Framework For Pathway Analysis In Genome Wide Association Studies

DOWNLOAD

Download A Bayesian Hierarchical Framework For Pathway Analysis In Genome Wide Association Studies PDF/ePub or read online books in Mobi eBooks. Click Download or Read Online button to get A Bayesian Hierarchical Framework For Pathway Analysis In Genome Wide Association Studies book now. This website allows unlimited access to, at the time of writing, more than 1.5 million titles, including hundreds of thousands of titles in various foreign languages. If the content not found or just blank you must refresh this page

A Bayesian Hierarchical Framework For Pathway Analysis In Genome Wide Association Studies

DOWNLOAD
Author : Lei Zhang
language : en
Publisher:
Release Date : 2018

A Bayesian Hierarchical Framework For Pathway Analysis In Genome Wide Association Studies written by Lei Zhang and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with Bayesian statistical decision theory categories.

The genome-wide association studies (GWAS) aim to identify genetic variants, typically single nucleotide polymorphisms (SNPs), associated with a disease/trait. A commonly used analytic strategy in GWAS is to test for association with one single SNP at a time. However, such a strategy lacks power to detect associations that are caused by joint effects of multiple variants, each with a modest effect of its own. Pathway analysis jointly tests the combined effects of all SNPs in all genes belonging to a molecular pathway. This analysis is usually more powerful than single-SNP analyses for detecting joint effects of variants in a pathway. Moreover, due to biological functionality of pathways, a significant result lends itself more easily to interpretation. In this dissertation, we develop a Bayesian hierarchical model that fully models the natural three-level hierarchy inherent in pathway structure, namely SNP—gene—pathway, unlike most other methods that use ad hoc ways of combining such information. We model the effects at each level conditional on the effects of the levels preceding them within the generalized linear model framework. This joint modeling allows detection of not only the associated pathways but also testing for association with genes and SNPs within significant pathways and significant genes in a hierarchical manner, which can be useful for follow-up studies. To deal with the high dimensionality of such a unified model, we regularize the regression coefficients through an appropriate choice of priors. We fit the model using a combination of Iteratively Weighted Least Squares and Expectation-Maximization algorithms to estimate the posterior modes and their standard errors. The inference is carried out in a hierarchical manner from pathways to genes to SNPs. Hierarchical false discovery rate (FDR) is used for multiplicity adjustment of the entire inference procedure. We also explore the utility of effective number of parameters proposed in the Bayesian literature in our context of multiplicity adjustment using the hierarchical FDR. To study the proposed approach, we conduct simulations with samples generated under realistic linkage disequilibrium patterns obtained from the HapMap project. We find that our method has higher power than some standard approaches in several settings for identifying pathways that have multiple modest-sized variants. Moreover, it can also pinpoint associated genes once a pathway is implicated, a feature unavailable in other methods. We also find that the use of the effective number of parameters can boost the power to detect associated genes and helps in distinguishing them from the null genes. We apply the proposed method to two GWAS datasets on breast and renal cancer.

Imaging Genetics

DOWNLOAD
Author : Adrian Dalca
language : en
Publisher: Academic Press
Release Date : 2017-09-22

Imaging Genetics written by Adrian Dalca and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-09-22 with Technology & Engineering categories.

Imaging Genetics presents the latest research in imaging genetics methodology for discovering new associations between imaging and genetic variables, providing an overview of the state-of the-art in the field. Edited and written by leading researchers, this book is a beneficial reference for students and researchers, both new and experienced, in this growing area. The field of imaging genetics studies the relationships between DNA variation and measurements derived from anatomical or functional imaging data, often in the context of a disorder. While traditional genetic analyses rely on classical phenotypes like clinical symptoms, imaging genetics can offer richer insights into underlying, complex biological mechanisms. - Contains an introduction describing how the field has evolved to the present, together with perspectives on its future direction and challenges - Describes novel application domains and analytic methods that represent the state-of-the-art in the burgeoning field of imaging genetics - Introduces a novel, large-scale analytic framework that involves multi-site, image-wide, genome-wide associations

Statistical Bioinformatics

DOWNLOAD
Author : Jae K. Lee
language : en
Publisher: John Wiley & Sons
Release Date : 2011-09-20

Statistical Bioinformatics written by Jae K. Lee and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-09-20 with Medical categories.

This book provides an essential understanding of statistical concepts necessary for the analysis of genomic and proteomic data using computational techniques. The author presents both basic and advanced topics, focusing on those that are relevant to the computational analysis of large data sets in biology. Chapters begin with a description of a statistical concept and a current example from biomedical research, followed by more detailed presentation, discussion of limitations, and problems. The book starts with an introduction to probability and statistics for genome-wide data, and moves into topics such as clustering, classification, multi-dimensional visualization, experimental design, statistical resampling, and statistical network analysis. Clearly explains the use of bioinformatics tools in life sciences research without requiring an advanced background in math/statistics Enables biomedical and life sciences researchers to successfully evaluate the validity of their results and make inferences Enables statistical and quantitative researchers to rapidly learn novel statistical concepts and techniques appropriate for large biological data analysis Carefully revisits frequently used statistical approaches and highlights their limitations in large biological data analysis Offers programming examples and datasets Includes chapter problem sets, a glossary, a list of statistical notations, and appendices with references to background mathematical and technical material Features supplementary materials, including datasets, links, and a statistical package available online Statistical Bioinformatics is an ideal textbook for students in medicine, life sciences, and bioengineering, aimed at researchers who utilize computational tools for the analysis of genomic, proteomic, and many other emerging high-throughput molecular data. It may also serve as a rapid introduction to the bioinformatics science for statistical and computational students and audiences who have not experienced such analysis tasks before.

Application Of Clinical Bioinformatics

DOWNLOAD
Author : Xiangdong Wang
language : en
Publisher: Springer
Release Date : 2016-03-31

Application Of Clinical Bioinformatics written by Xiangdong Wang and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-03-31 with Medical categories.

This book elucidates how genetic, biological and medical information can be applied to the development of personalized healthcare, medication and therapies. Focusing on aspects of the development of evidence-based approaches in bioinformatics and computational medicine, including data integration, methodologies, tools and models for clinical and translational medicine, it offers an essential introduction to clinical bioinformatics for clinical researchers and physicians, medical students and teachers, and scientists working with human disease-based omics and bioinformatics. Dr. Xiangdong Wang is a distinguished Professor of Medicine. He is Director of Shanghai Institute of Clinical Bioinformatics, Director of Fudan University Center for Clinical Bioinformatics, Deputy Director of Shanghai Respiratory Research Institute, Director of Biomedical Research Center, Fudan University Zhongshan Hospital, Shanghai, China; Dr. Christian Baumgartner is a Professor of Health Care and Biomedical Engineering at Institute of Health Care Engineering with European Notified Body of Medical Devices, Graz University of Technology, Graz, Austria; Dr. Denis Shields is a Professor of Clinical Bioinformatics at Conway Institute, Belfield, Dublin, Ireland; Dr. Hong-Wen Deng is a Professor at Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, USA; Dr. Jacques S Beckmann is a Professor and Director of Section of Clinical Bioinformatics, Swiss Institute of Bioinformatics, Switzerland.

The Microbiome In Health And Disease

DOWNLOAD
Author :
language : en
Publisher: Academic Press
Release Date : 2020-05-29

The Microbiome In Health And Disease written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-05-29 with Science categories.

The Microbiome in Health and Disease, Volume 171 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Microbiome in health and disease, CNS development and microbiome in infants, A gut feeling in ALS, Microbiome (Virome) and virus infection, Bugs and Drugs: microbiome in medicine metabolism, Immunity, T cells, and microbiome, Salmonella (Bacterial) infection and cancer: of mice and men, and many other highly researched topics. - Provides a novel theme and multiple disciplinary topics of microbiome research in basic and translational studies - Presents an updated collection on bacteria, virus, fungi and their interactions in microbiome - Includes a timely discussion on the tools and methods used for modeling and analysis of microbiome data

Artificial Intelligence And Bioinformatics Applications For Omics And Multi Omics Studies

DOWNLOAD
Author : Angelo Facchiano
language : en
Publisher: Frontiers Media SA
Release Date : 2024-02-07

Artificial Intelligence And Bioinformatics Applications For Omics And Multi Omics Studies written by Angelo Facchiano and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-02-07 with Science categories.

Gene Regulation Explored By Systems Biology In Livestock Science

DOWNLOAD
Author : Andressa Oliveira De Lima
language : en
Publisher: Frontiers Media SA
Release Date : 2022-04-27

Gene Regulation Explored By Systems Biology In Livestock Science written by Andressa Oliveira De Lima and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-04-27 with Science categories.

Computational Epigenetics In Human Diseases Cell Differentiation And Cell Reprogramming Volume Ii

DOWNLOAD
Author : Yongchun Zuo
language : en
Publisher: Frontiers Media SA
Release Date : 2022-03-31

Computational Epigenetics In Human Diseases Cell Differentiation And Cell Reprogramming Volume Ii written by Yongchun Zuo and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-03-31 with Science categories.

Journal Of The American Statistical Association

DOWNLOAD
Author :
language : en
Publisher:
Release Date : 2009

Journal Of The American Statistical Association written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009 with Electronic journals categories.

Dissertation Abstracts International

DOWNLOAD
Author :
language : en
Publisher:
Release Date : 2004

Dissertation Abstracts International written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with Dissertations, Academic categories.