Copy number differences between groups
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3.2 years ago
neuro3030 ▴ 50

Analogous to differential expression with RNA data, is there a statistic or tool to analyze the frequency of copy number alterations between two groups?

I had imagined this to be a Chi-square performed like 20,000 times (each gene) to see if that particular gene is deleted more than one would expect by chance. However, one cannot assume independence of the events since genes are often recurrently deleted together owing to deletion of large regions.

Any suggestions?

CNA Differential GISTIC • 1.2k views
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You might want to reference table 1 here and see which flavor you want https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394692/

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Thanks. I already used TCGA data to run GISTIC, and I now have the thresholds for copy number alterations: -2, -1, 0, 1, 2. I would like to compare the frequency of these for each gene, between two groups. There are about 20,000 genes. How do I determine which genes are more frequently deleted or amplified in group 1 vs group 2?

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Hi, I have the same question. Could you find a way to determine which genes are more frequently deleted or amplified in group 1 vs group 2?

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Any update on this? I think it is a very relevant question

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Dif you find a way to do this?

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