This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison, Spring 2012.
ALS Microarray Analysis
What is a microarray?
A microarray is an experiment using a chip to measure the expression levels of many genes in a given sample compared to a control. GEO is a database that compiles microarray data in order to make these large data sets available to other researchers.
Microarray analysis SOD1 mutant mice
Below is an example of one microarray experiment undertaken to help better understand how mutant SOD1 leads to motor neuron degeneration. The researchers looked at the expression levels of 22,690 genes in the motor neurons of SOD1 mutant mice at three ages: 60, 90, and 120 days old [1]. Microarray data is presented in heat maps with one line for each gene in each treatment. Here, pink shows higher expression in SOD1 mutant motor neurons than in wild type at the same age.
When you take a closer look at a region of this map, the treatments and genes are more clearly displayed. Here is an example of a group of genes that are upregulated in older SOD1 mutant mice. (Click to enlarge.)
Analysis
There are many groups of genes upregulated at each of the 60-, 90-, and 120-day mutant SOD1 mice including genes related to cell death, cell adhesion, cell cycle and metabolism among others. From their data, these researchers proposed a model in which an early increase in general transcription leads to an increase in mitochondrial workload and a subsequent increase in reactive oxygen species. Later, these increases lead to a general disruption of cell function, and protein degradation and cell death genes are upregulated [1].
This is just one example of the type of data that can be obtained through large scale approaches like microarrays. The resulting models can then be tested through further experiments.
This is just one example of the type of data that can be obtained through large scale approaches like microarrays. The resulting models can then be tested through further experiments.
1. Ferraiuolo L, Heath PR, Holden H, Kasher P, Kirby J, Shaw PJ. (2007). Microarray analysis of the cellular pathways involved in the adaptation to and progression of motor neuron injury in the SOD1 G93A mouse model of familial ALS. J Neurosci 27 (34): 9201-19. PMID:17715356