MBASED: allele-specific expression detection in cancer tissues and cell lines

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Mayba, Oleg, Gilbert, Houston N, Liu, Jinfeng, Haverty, Peter M, Jhunjhunwala, Suchit, Jiang, Zhaoshi, Watanabe, Colin, Zhang, Zemin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165366/
https://www.ncbi.nlm.nih.gov/pubmed/25315065
http://dx.doi.org/10.1186/s13059-014-0405-3
_version_ 1782335093635809280
author Mayba, Oleg
Gilbert, Houston N
Liu, Jinfeng
Haverty, Peter M
Jhunjhunwala, Suchit
Jiang, Zhaoshi
Watanabe, Colin
Zhang, Zemin
author_facet Mayba, Oleg
Gilbert, Houston N
Liu, Jinfeng
Haverty, Peter M
Jhunjhunwala, Suchit
Jiang, Zhaoshi
Watanabe, Colin
Zhang, Zemin
author_sort Mayba, Oleg
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0405-3) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-4165366
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-41653662014-09-26 MBASED: allele-specific expression detection in cancer tissues and cell lines Mayba, Oleg Gilbert, Houston N Liu, Jinfeng Haverty, Peter M Jhunjhunwala, Suchit Jiang, Zhaoshi Watanabe, Colin Zhang, Zemin Genome Biol Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0405-3) contains supplementary material, which is available to authorized users. BioMed Central 2014-08-07 2014 /pmc/articles/PMC4165366/ /pubmed/25315065 http://dx.doi.org/10.1186/s13059-014-0405-3 Text en © Mayba et al.;licensee BioMed Central 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Mayba, Oleg
Gilbert, Houston N
Liu, Jinfeng
Haverty, Peter M
Jhunjhunwala, Suchit
Jiang, Zhaoshi
Watanabe, Colin
Zhang, Zemin
MBASED: allele-specific expression detection in cancer tissues and cell lines
title MBASED: allele-specific expression detection in cancer tissues and cell lines
title_full MBASED: allele-specific expression detection in cancer tissues and cell lines
title_fullStr MBASED: allele-specific expression detection in cancer tissues and cell lines
title_full_unstemmed MBASED: allele-specific expression detection in cancer tissues and cell lines
title_short MBASED: allele-specific expression detection in cancer tissues and cell lines
title_sort mbased: allele-specific expression detection in cancer tissues and cell lines
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165366/
https://www.ncbi.nlm.nih.gov/pubmed/25315065
http://dx.doi.org/10.1186/s13059-014-0405-3
work_keys_str_mv AT maybaoleg mbasedallelespecificexpressiondetectionincancertissuesandcelllines
AT gilberthoustonn mbasedallelespecificexpressiondetectionincancertissuesandcelllines
AT liujinfeng mbasedallelespecificexpressiondetectionincancertissuesandcelllines
AT havertypeterm mbasedallelespecificexpressiondetectionincancertissuesandcelllines
AT jhunjhunwalasuchit mbasedallelespecificexpressiondetectionincancertissuesandcelllines
AT jiangzhaoshi mbasedallelespecificexpressiondetectionincancertissuesandcelllines
AT watanabecolin mbasedallelespecificexpressiondetectionincancertissuesandcelllines
AT zhangzemin mbasedallelespecificexpressiondetectionincancertissuesandcelllines

Ejemplares similares