The TCGA provisional data were used to evaluate the prognostic effect of gene sets derived from specific cell clusters. The provisional gene expression and survival data of the TCGA were accessed using CBioPortal. We used Limma to perform differential expression gene analysis for each cluster and defined genes with more than two‐fold increase in expression in one cluster compared to the other clusters as “signature genes.” For the signature gene sets of each cluster, we calculated a “gene signature score” for each patient using fold‐change values for each gene in the signature to weigh genes in calculations of the average. Then, patients were grouped into high‐ and low‐expression groups by the median value of the “gene signature score.” To correct for clinical covariates including age and histological grade, we performed multivariable analyses using Cox proportional hazard survival models to obtain the hazard ratio and adjusted P‐value.

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.