This web page was produced as an assignment for Genetics 564, an undergraduate course at UW-Madison. http://genetics564.weebly.com/
GEO Expression
Genes are not all constitutively active at the same time. Genes are expressed at different levels and locations at specific times in the body. Gene expression is a valuable experimental tool that can be used to investigate variables in different experimental conditions. Where and when genes are expressed all depend on the conditions in the cell. Therefore, gene expression can tell you a lot about what is occurring within certain cells.
In particular, monitoring gene expression differences between mutant (ill-functioning) genes and the normal, wild-type version of your gene can help you determine which cells are associated with the disease. For example, pathological and healthy cells can be monitored for varying gene expression using single-cell RNA-sequencing. The three types of analyses you can perform with gene expression are within the cell type, between cell types, and between tissues. |
GEO Profiles
GEO Profiles stores gene expression and presents it in chart form with the level of gene expression across all of the samples in a DataSet (1-2) . The experimental context is in the bars on the bottom, which allows you to compare gene expression changes in different experimental contexts.
Example GEO profile found for PTPN2
Analysis
Gene expression is a very useful tool for analyzing differences between your wild-type and mutant gene. Monitoring changes in gene expression and using GEO profiles allow you determine what genes are being down- or up-regulated in your gene of interest. This can be of particular use with PTPN2 and determining gene expression differences in the Crohn's Disease mutant and wild-type.
References
- http://genetics564.weebly.com/gene-expression-analysis.html
- GEO Profiles http://www.ncbi.nlm.nih.gov/geoprofiles/