Caryoscope: Putting Microarray Data in Chromosomal Context

Microarrays are wonderful tools for seeing global patterns of gene expression under different conditions. Plenty of software exists to make sense of the data, but what if you want to correlate expression patterns with location? Perhaps Caryoscope can help.

Rather than forcing users to stare at endless columns of data or the traditional Rorschach-like microarray readout, Caryoscope http://caryoscope.stanford.edu overlays color-coded microarray data onto a chromosomal map. "It allows you to view gene-expression data within the context of the genomic structure," says Gavin Sherlock, the Stanford University geneticist who oversaw Ihab Awad, the program's primary author.

Researchers can download Caryoscope (a component of the Generic Model Organism Database project) as a Java applet (current version 0.3.9) for local use, or run it remotely on Stanford's servers. Accepted file formats include tab-delimited, comma-delimited, and GFF (general file format, an emerging standard for microarray data), all of which can be generated by...