Eqtl Analysis: Methods and Protocols

ISBN-13: 9781071600283 / Angielski / Miękka / 2021 / 252 str.

Xinghua Mindy Shi

Spis treści

Part I: Foundations

1. Introductory Methods for eQTL Analyses

Conor Nodzak

 

2. Performing QTL and eQTL Analyses with the R-package GenomicTools

Daniel Fischer

 

3. eQTL Mapping using Transcription Factor Affinity

Elisa Mariella, Elena Grassi, and Paolo Provero

 

4. Identification and Quantification of Splicing Quantitative Trait Loci

Ankeeta Shah and Yang I. Li

 

5. Genome-wide Composite Interval Mapping (GCIM) of Expressional Quantitative Trait Loci in Backcross Population

Yuan-Ming Zhang

 

6. Combining eQTL and SNP Annotation Data to Identify Functional Noncoding SNPs in GWAS Trait-associated Regions

Stephen A. Ramsey, Zheng Liu, Yao Yao, and Benjamin Weeder

 

7.  Statistical and Machine Learning Methods for eQTL Analysis

Junjie Chen and Conor Nodzak

 

8. Sparse Regression Models for Unraveling Group and Individual Associations in eQTL Mapping

Wei Cheng, Xiang Zhang, and Wei Wang

 

9. Exploring Bayesian Approaches to eQTL Mapping through

Probabilistic Programming

Dimitrios V. Vavoulis

 

10. High-order Association Mapping for Expression Quantitative Trait Loci

Huaizhen Qin, Weiwei Ouyang, and Jinying Zhao

 

11. Integration of Multi-omics Data for Expression Quantitative Trait Loci (eQTL) Analysis and eQTL Epistasis

Mingon Kang and Jean Gao

 

12. Sparse Partial Least Squares Methods for Joint Modular Pattern Discovery

Jinyu Chen and Shihua Zhang

 

Part II: Applications

13. Expression Quantitative Trait Loci (eQTL) Analysis in Cancer

Yaoming Liu, Youqiong Ye, Jing Gong, and Leng Han

 

14. QTL Analysis Beyond eQTLs

Jia Wen and Conor Nodzak

 

15. Quantitative Trait Loci (QTL) Mapping

Kara E. Powder

 

16. Expression Quantitative Trait Loci Analysis in Multiple Tissues

Gen Li

 

17. Tissue Specific eQTL in Zebrafish

Kimberly Dobrinski

Blurb

This volume details state-of-art eQTL analysis, where interdisciplinary researchers are provided both theoretical and practical guidance to eQTL analysis and interpretation. Chapters guide readers through methods and tools for eQTL and QTL analysis and the usage of such analysis in various scenarios. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, eQTL Analysis: Methods and Protocols to ensure successful results in the further study of this vital field.