Introduction to Bioinformatics - COIN81
COIN 81 Week Nine
This week we'll study microarrays, including Gene Chips (DNA), SNP chips (SNPs), Protein arrays, glycan arrays, as well as Copy Number Variation (CNV) and association analysis. Microarray analysis, gene chips, SNP chips (rapid genotyping) and glycan arrays. There is also a rapidly growing effort in miRNA (micro RNA) profiling.
DNA Microarray - Gene Chips. Try working through this short Flash animation on the basics of DNA microarray technology. There are also primers on DNA microarray technology at NCBI. Study both of these before going any further.
SNP array - SNP arrays are a rapidly growing tool and methodology used in 'genotyping' individuals. There is also a primer on SNPs at NCBI entitled ' Variations on a Theme' that will help you work through this science.
Copy Number Variations - Copy Number Variation (CNV) is a recent focus of study using increasingly sophisticated approaches in biotechnology. There is a small but growing body of evidence that copy number variation may be partly responsible for some diseases and syndromes.
Protein array - Protein arrays are used to analyze extracts from cells using antibody bonding to a microarray plate, similar to DNA (gene chip) arrays. It is more complex and less sensitive that DNA microarrays, but growing in power, speed, and sensitivity.
Glyco gene chips - Glycan arrays are used to detect bonding to glycoproteins which are bound to silicon microarrays in a similar manner as DNA and protein arrays. Glycan arrays have been use din the analysis of influenza binding, i.e. serotype specificity to particular cells (with cell surface glycoproteins) and especially to test whether a mutation in an HA and or NA protein will infer greater infection and pathogenicity / virulence to a particular host population.
MicroRNA profiling - here is an entirely new methodology for understanding cellular processes at the level of the transcriptome. MicroRNA (miRNA) are an essential element in gene regulation and the proper functioning of the cell.