DNA microarrays used to be the leading technology for genome-wide studies, until Next Generation Sequencing (NGS) approaches took over and often replaced microarrays. However, DNA microarrays are still used for certain applications, and occasionally scientists wish to re-analyze old microarray datasets.
Throughout the years, the Bioinformatics Core Facility has analyzed numerous microarray experiments of various platforms (Affymetrix, Illumina, Agilent, Nimblegene, custom spotted arrays etc.) and types. Our expertise covers various applications of DNA microarrays, including:
- Differential gene expression, at the exon, gene and pathway levels
- Identification of chromosomal aberrations (CNV, CGH, LOH)
- Identification of protein binding sites in DNA or RNA samples (e.g. ChIP on chip)
- Genetic studies using SNP and CNV arrays: linkage, association, cytogenetics, homozygosity & shared haplotype analyses, pharmacogenomics.
These analyses are complemented by advanced clustering analyses, as well as functional analyses, gene ontology and pathway enrichment, and overlay on protein-protein interaction networks.