Identification of allele-specific alternative mRNA processing via transcriptome sequencing

ABSTRACT: Establishing the functional roles of genetic variants remains a significant challenge in the post-genomic era. Here, we present a method, allele-specific alternative mRNA processing (ASARP), to identify genetically influenced mRNA processing events using transcriptome sequencing (RNA-Seq) data. The method examines RNA-Seq data at both single nucleotide and whole-gene/isoform levels to identify allele-specific expression (ASE) and existence of allele-specific regulation of mRNA processing. We applied the methods to data obtained from the human glioblastoma cell line U87MG and primary breast cancer tissues and found that 26M-bM-^@M-^S45% of all genes with sufficient read coverage demonstrated ASE, with significant overlap between the two cell types. Our methods predicted potential mechanisms

ORGANISM(S): Homo sapiens

SUBMITTER: Gang Li 

PROVIDER: E-GEOD-29738 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress