Chromosome Color Theme

The Chromosome Color Theme process creates a settings (.sas) file from a text file that defines a chromosome color theme. This settings file can be used for display of the Chromosome Color Plot in the JMP Genomics Browser process.

The output settings file defining the input Chromosome Text Data Set and the Color Theme is saved as a .sas file for subsequent use.

What do I need?

A single .txt input file is required, which contains information about the genome of interest, such as:

•	the chromosome or other grouping variable,

•	the start and stop positions of cytobands, genes, or other aspects of the genome, and

•	variables by which to color and label the start to stop position areas.

The input text file can be downloaded from the Gene Expression Omnibus (GEO) or the UCSC Genome Browser. Alternatively, you can create your own file using bins across positions of interest using the JMP Genomics Browser process. The file must meet the following conditions:

•	it is tab delimited,

•	its first row contains column headings, and

•	data begins on the second row.

The cytoBandIdeoHuman.txt file, opened in JMP, is shown below. This file, which was downloaded from the UCSC Genome Browser to the JMP Genomics Sample Data\UCSC\Cytoband directory, is shipped with JMP Genomics.

The input file must have certain columns in order to properly define the genomic features. Columns must list:

•	chromosome,

•	chromosomal location,

•	feature name, and

•	a coloring variable.

In the cytoBandIdeoHuman.txt file shown above, the location of Human chromosomal G-bands are defined by the chromStart and chromEnd variables. The gieStain variable, listing giemsa staining properties of the cytobands, can be used as the coloring variable.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.

Output/Results

Refer to the Chromosome Color Theme output documentation for detailed descriptions and guides to interpreting your results.