What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants.

ABSTRACT: Many problems of modern genetics and functional genomics require the assessment of functional effects of sequence variants, including gene expression changes. Machine learning is considered to be a promising approach for solving this task, but its practical applications remain a challenge due to the insufficient volume and diversity of training data. A promising source of valuable data is a saturation mutagenesis massively parallel reporter assay, which quantitatively measures changes in transcription activity caused by sequence variants. Here, we explore the computational predictions of the effects of individual single-nucleotide variants on gene transcription measured in the massively parallel reporter assays, based on the data from the recent "Regulation Saturation" Critical Assessment

SUBMITTER: Penzar DD 

PROVIDER: S-EPMC6834773 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature