Caryoscope is a software package that allows you to display and explore numerical data as a function of genomic position. For example, Caryoscope has been used to "draw" microarray data onto a set of chromosomes so that changes in DNA copy number can identify regions of chromosome loss or duplication within the genome of tumor cells (Nat Genet. 1999 Sep;23(1):41-6). In addition, microarray data measuring mRNA expression levels can also be visualized in a genomic context using Caryoscope (PNAS 2002 Dec 10;99(25):16144-9). Data viewed with Caryscope need not be limited to microarray data -- any type of numerical data that can be represented as a function of genomic position can be visualized using Caryoscope.

In order to display such data, the lengths of each chromosome as well as the chromosomal location and values for each data element (e.g., the chromosomal coordinates and log ratio data for clones on a cDNA microarray) must be supplied in a suitable input file. See Chapter 2, Tutorial for help in getting started.

Below is a screenshot of Caryoscope in action: