title: MBASED: allele-specific expression detection in cancer tissues and cell lines.
abstract: Allele-specific gene expression, ASE, is an important aspect of gene regulation. We developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq data that aggregates information across multiple single nucleotide variation loci to obtain a gene-level measure of ASE, even when prior phasing information is unavailable. MBASED is capable of one-sample and two-sample analyses and performs well in simulations. We applied MBASED to a panel of cancer cell lines and paired tumor-normal tissue samples, and observed extensive ASE in cancer, but not normal, samples, mainly driven by genomic copy number alterations.
authors.forename: Oleg
authors.initials: O
authors.lastname: Mayba
authors.forename: Houston N
authors.initials: HN
authors.lastname: Gilbert
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Liu
authors.forename: Peter M
authors.initials: PM
authors.lastname: Haverty
authors.forename: Suchit
authors.initials: S
authors.lastname: Jhunjhunwala
authors.forename: Zhaoshi
authors.initials: Z
authors.lastname: Jiang
authors.forename: Colin
authors.initials: C
authors.lastname: Watanabe
authors.forename: Zemin
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D000483:Alleles; D016010:Binomial Distribution; D019295:Computational Biology / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017423:Sequence Analysis, RNA; D012984:Software; D014407:Tumor Cells, Cultured