2017/09/06 by Steven P. Ellis, Ellis, Steven P.
Biochemistry, Genetics and Molecular Biology · Computer Science · #62M99 #92C40 #Applications (stat.AP) #Bioinformatics and Genomic Networks #FOS: Biological sciences #FOS: Computer and information sciences #Gene expression and cancer classification #Quantitative Methods (q-bio.QM) #Topological and Geometric Data Analysis
paper · pdf · doi:10.48550/arxiv.1709.01753
openalex publication_date 2017/09/06 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The topological data analysis method "concurrence topology" is applied to mutation frequencies in 69 genes in glioblastoma data. In dimension 1 some apparent "mutual exclusivity" is found. By simulation of data having approximately the same second order dependence structure as that found in the data, it appears that one triple of mutations, PTEN, RB1, TP53, exhibits mutual exclusivity that depends on special features of the third order dependence and may reflect global dependence among a larger group of genes. A bootstrap analysis suggests that this form of mutual exclusivity is not uncommon in the population from which the data were drawn.