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broadinstitute / gistic2

Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
MIT License
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genes in wide peak #15

Closed stroke1989 closed 2 years ago

stroke1989 commented 2 years ago

Hi, Thanks for this wonderful tool. I used GISTIC2 to analyze my WES data, and I got several file, including a file named "amp_genes.conf_95.txt", and a file named "all_data_by_genes.txt", I found the genes in wide peak in del_genes.conf_95.txt did not matched the genes in wide peak in all_data_by_genes.txt, details in below:

amp_genes all_data_by_genes

many genes were omitted in file amp_genes.conf_95.txt

additionally, the gene EGFR locats in 7p11.2, but in the file amp_genes.conf_95.txt, EGFR located in 7q36.1. Similarly, BRAF locates in 7q34, but in the amp_genes.conf_95.txt, BRAF located in 7q31.2. Hope your reponse! Appreciate

stevenschumacher commented 2 years ago

The genes listed in the all_data_by_gene table are all of the genes in the reference genome used by the GISTIC analysis. The genes listed in the amp_genes and del_genes tables are limited to those that fall within the peak regions of significant copy number alterations. The cytoband of a gene is where the gene is located. The cytoband of a peak is the cytoband where the maximally significant part of the peak is located. In your case, the peak is wide enough that it spans several cytobands.

aHEUREU commented 3 weeks ago

But it is confusing to identify the cytoband location of significant altered genes. Is there any parameter to improve the resolution of cytiband positions or I can only manually correct them? Thank you!