Epigenetics and Gene Regulation
This module jointly concerns statistical genetic principles around epigenetics and gene regulation. Lectures and practical sessions will introduce students to the methodology for studying both germline and somatic epigenetic processes, with particular attention to methylation profiling. Additional topics will include methylation QTL analysis, epigenome-wide association studies, and methylation risk scores, and aging effects.
The second half of the course focuses on methods for predicting gene expression and its association with complex traits and diseases. We will cover TWAS, ChIP-Seq analysis, regulatory motif discovery, and machine learning approaches to inference of non-coding DNA function, and integrative analysis with inferred non-coding DNA functional and GWAS annotations. Modules IG3 and IG4 cover single cell gene expression profiling and network and pathway analysis respectively.
Learning Objectives: After attending this module, participants will be able to:
- Understand the difference between germline and somatic epigenetic phenomena.
- Know the major modes of epigenetic profiling, including methylation, chromatin accessibility, histone modification, and chromatin contacts.
- Perform a methylation profiling analysis, as well as compute mQTL and methylation risk scores.
- Understand the methods and tools used in TWAS and be able to perform a TWAS analysis.
- Be able to conduct ChIP-Seq analysis and identify Transcription Factor Binding Sites (TFBS).
- Understand the theory behind Deep-SEA, LINSIGHT, and know how to use their non-coding DNA functional predictions to prioritize potential causal variants.
Course Dates
- Wed June 4, 1:30 p.m. – 5:00 p.m. EST
- Thu June 5, 8:30 a.m. – 5:00 p.m. EST
- Fri June 6, 8:30 a.m. – 5:00 p.m. EST
Instructors
- Karen Conneely
- Jingjing Yang
- Alicia Smith
Suggested Course Pairings
Integrative Genomics Stream
- Module INT1: Genetics and Genomics
- Module IG1: Genetics and Genomics
- Module IG3: Gene Expression
- Module IG4: Gene Networks and Pathways
Course Materials
Please email sisg@biosci.gatech.edu for free access.
About the Instructors
Karen Conneely is an Associate Professor in the Department of Human Genetics at Emory University in Atlanta. She is particularly interested in the role of DNA methylation as mediator between genetic variation, environment and phenotype. Ongoing work in her lab uses computational approaches to understand the relationship between multiple epigenetic mechanisms, gene expression, and human aging. Access Karen’s publications here. She will be assisted by Emory colleague Alicia Smith, whose lab employs methylation profiling to study the regulation of behavioral and psychological traits.
Jingjing Yang is also an Associate Professor in the Department of Human Genetics at Emory University in Atlanta. The Yang Lab is developing statistical and computational methods and tools for quantitative genomics data analysis and biomedical data analysis. Her TIGAR and OTTERS software supports Transcriptome-wide Association Studies. Learn more about Jingjing’s work here.