Tables of basic information about the genomic regions (peaks) that GISTIC

determined to be significantly amplified or deleted. These describe three

kinds of peak boundaries, and list the genes contained in two of them. The

region start and region end columns (along with the chromosome column)

delimit the entire area containing the peak that is above the significance

level. The region may be the same for multiple peaks. The peak start and end

delimit the maximum value of the peak. The extended peak is the peak

determined by robust, and is contained within the wide peak reported in

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

A table of per-arm statistical results for the data set. Each arm is a row

in the table. The first column specifies the arm and the second column

counts the number of genes known to be on the arm. For both amplification

and deletion, the table has columns for the frequency of amplification or

deletion of the arm, and a Z score and Q value.

A table of chromosome arm amplification levels for each sample. Each row is

a chromosome arm, and each column a sample. The data are in units of absolute

Broad Values By Arm (broad_values_by_arm.txt)

A gene-level table of copy number values for all samples. Each row is the

data for a gene. The first three columns name the gene, its NIH locus ID,

and its cytoband - the remaining columns are the samples. The copy number

values in the table are in units of (copy number -2), so that no

amplification or deletion is 0, genes with amplifications have positive

values, and genes with deletions are negative values. The data are converted

from marker level to gene level using the extreme method: a gene is assigned

the greatest amplification or the least deletion value among the markers it

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number data similar to the

output, but using only broad events with lengths greater than the  broad

length cutoff. The structure of the file and the methods and units used for