RT Journal Article
SR Electronic
T1 GeTallele: a mathematical model and a toolbox for integrative analysis and visualization of DNA and RNA allele frequencies
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 491209
DO 10.1101/491209
A1 Piotr Słowiński
A1 Muzi Li
A1 Paula Restrepo
A1 Nawaf Alomran
A1 Laim Spurr
A1 Christian Miller
A1 Krasimira Tsaneva-Atanasova
A1 Anelia Horvath
YR 2018
UL http://biorxiv.org/content/early/2018/12/09/491209.abstract
AB Motivation Asymmetric allele expression typically indicates functional and/or structural features associated with the underlying genetic variants. When integrated, RNA and DNA allele frequencies can reveal patterns characteristic for a wide-range of biological traits, including ploidy changes, genome admixture, allele-specific expression and gene-dosage transcriptional response.Results To assess RNA and DNA allele frequencies from matched sequencing datasets, we introduce GeTallele: a toolpack that provides a suit of functions for integrative analysis, statistical assessment and visualization of Genome and Transcriptome allele frequencies. We demonstrate this functionality across cancer DNA and RNA sequencing sets by detecting novel relationships between encoded and expressed variation that can improve solving of genome composition and expression regulation. In addition, we explore GeTallele as a tool for preliminary assessment of large-scale genomic alterations from RNA-sequencing datasets.Availability GeTallele is implemented as a Matlab toolbox available at: https://git.exeter.ac.uk/pms210/getalleleContact P.M.Slowinski{at}exeter.ac.ukSupplementary information Supplementary data are available at Bioinformatics online.