PGY/PHA 617 Physiological Genomics: Microarray gene expression profiling
Co-course directors:
Tim McClintock, Physiology, 323-1083, mcclint@uky.edu
Kuey-Chu Chen, Molecular and Biomedical Pharmacology, 323-6241, kueyc@uky.edu
Course Description. This course, designed for second and third year graduate students, teaches the study of function by global analysis of gene expression and gene regulation. It not only emphasizes the technical aspects of measuring gene expression and gene regulation with microarray and deep sequencing techniques, but also incorporates examples where such studies have had a significant impact on understanding the function or dysfunction of physiological systems.
Prerequisites: IBS604 Cell Signaling and IBS602 Biomolecules and Molecular Biology, or their equivalents. Suggested companion course: BIO520 Bioinformatics
Major themes.
1. UniGene, Entrez Gene, BLAST and other NCBI bioinformatics tools
2. Comparison of mRNA expression profiling techniques
3. Microarray analysis of changes in alternative splicing
4. Design and statistical analysis of microarray experiments
5. Bioinformatics of microarray data
6. Analysis of genetic variation: copy number and single nucleotide polymorphisms (SNPs)
7. Epigenetics and the control of gene expression
Course objectives. Students will learn to:
1. Extract detailed information about a gene and its encoded protein from databases.
2. Design an expression profiling or epigenetics experiment and choose the appropriate method.
3. Analyze results, including the identification of functional processes and pathways in the data.
4. Construct hypotheses and tests of system-wide physiological responses.
5. Investigate epigenetic regulation of genes.
Methods of instruction. Approximately 15 hours of the instruction will be didactic lecture. The remainder of the course uses the computer lab to allow hands-on instruction in on-line bioinformatics tools, microarray data analysis, and data visualization.