List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

<span class="parameter">Arm Level Peel Off</span>

Segmented copy number profiles in the input data

The all lesions file summarizes the results from the GISTIC run. It contains data

about the significant regions of amplification and deletion as well as which

samples are amplified or deleted in each of these regions. The identified regions

are listed down the first column, and the samples are listed across the first

Columns 1-9 present the data about the significant regions as follows:

Unique Name: A name assigned to identify the region.

Descriptor: The genomic descriptor of that region.

Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes.  These are listed in genomic coordinates and marker (or probe) indices.

Peak Limits: The boundaries of the region of maximal amplification or deletion.

Region Limits: The boundaries of the entire significant region of amplification or deletion.

Q values: The Q value of the peak region.

Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Each of the analyzed samples is represented in one of the columns following the

lesion data (columns 10 through end). The data contained in these columns varies

The first section can be identified by the key given in column 9 - it starts in

row 2 and continues until the row that reads 'Actual Copy Change Given.' This

section contains summarized data for each sample.  A '0' indicates that the

copy number of the sample was not amplified or deleted beyond the threshold