I am trying to understand the HG-U95 chip microarray expression data which is using in the GSEA. I have understood the parameter in the p53 data set. It has 50 columns, first 17 columns are expressed as WT(Wild Type) and other 33 columns are expressed as MUT(Mutation). Rows are represented as no of features (genes) and values are represented as the expression values. But I have following questions about the parameters and values in that dataset.
How is this dataset differentially expressed as WT and MUT?
What is the biological meaning of this expression value?
Do you mean that you want to conduct the differential expression yourself, and that you want to understand how to do this? 'WT' is 'wild type', i.e., normal or healthy. 'MUT' will most likely mean those who have a mutation in TP53. Given the vast numbers of roles that TP53 has in DNA repair, cell cycle activity, etc., the expression profiles of these two groups of people will most likely differ. I don't know what the samples are in the study to which you allude, but they are most likely tumour samples, given TP53's role in tumourigenesis. However, heterozygous germline mutations in TP53 can also result in Li Fraumeni Syndrome.
To infer biological meaning from this, it is better to assume that the values that you see in the healthy individuals reflect a 'healthy' level of expression. Genes that are are statistically significantly higher or lower than these healthy levels can be assumed to have higher or lower relative expression in situations where the individual has TP53 mutations.
