The genomic and level 3 molecular profiling data of the PDAC patients were downloaded from The Cancer Genome Atlas (TCGA) database ( Copy number variation was assessed from the Affymetrix genome-wide human SNP array 6.0 platform using GISTIC2.0 (Version 2.0.22). Somatic mutations, single-nucleotide variants (SNVs), small insertion, and deletion were determined by Mutect. Fractions of single nucleotide substitutions in the six possible mutation classes (ie, C>T, C>A, C>G, A>G, A>C, and A>T) were calculated for each sample. Tumor mutational burden (TMB) was defined as the number of somatic, coding, base substitution, and indel mutations per mega base of genome examined. The nonparametric Mann-Whitney U-test was used to determine the significance in TMB difference between two populations. The R software package Limma was used to identify differentially expressed genes. Gene set enrichment analysis was performed using the GSEA software. Gene ontology and pathway analyses were performed with DAVID (

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

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.