Analysis of microarray data .ppt

Analysis of microarray data Introduction Microarrays are chips which measure whether genes are switched on or off in cells. They can be used to detect sets of genes responsible for genetic diseases such as cancer. This lecture: introduce microarray technology discuss a few applications introduce statistical and computational techniques for analysing microarray data Gene expression All cells in an organism have the same genomic DNA. Distinct cellular identities are due to differences in gene expression transcription translation of gene . Whether a gene is transcribed is often determined by the presence/ absence of other genes products esp. proteins … … so genes interact in complex networks: gene A switches on B, which turns off C which upregulates increases A, … Hence perturbations to single gene can lead to changes in expression of many genes. Functional genomics Next step after sequencing of human genome: understand connection between DNA sequence phenotypic actual characteristics of organism. This is complex, because proteins and genes act in highly connected networks and signalling pathways in an orchestrated manner. Traditionally molecular biology has worked on a “one gene one function” basis experiments tend to study the effects of a single gene/ few genes at a time, but... Microarray chips …microarrays can measure many genes at once. Microarray chips are commonly glass slides with a matrix of spots printed using eg. dot matrix technology on to them. A spot contains millions of identical molecules of DNA or oligonucleotide the probes , which will bind a specific DNA sequence, such as the cDNA of a gene. The glass slides can contain 1000s of spots, each recognising a different sequence, eg. one spot for every gene in the human genome. Microarray experiments Since almost all mRNA protein, total mRNA of cell ~ genes expressed. Mash up cells and extract mRNA. Reverse transcribe RNA ? cDNA can be heated to make single-stranded . Label cDNA fro