Identification of regulatory variants of carboxylesterase 1 (CES1): A proof‐of‐concept study for the application of the Allele‐Specific Protein Expression (ASPE) assay in identifying cis‐acting regulatory genetic polymorphisms
Sign Up to like & getrecommendations! Published in 2022 at "Proteomics"
DOI: 10.1002/pmic.202200176
Abstract: It is challenging to study regulatory genetic variants as gene expression is affected by both genetic polymorphisms and non‐genetic regulators. The mRNA allele‐specific expression (ASE) assay has been increasingly used for the study of cis‐acting… read more here.
Keywords: regulatory variants; allele specific; expression; acting regulatory ... See more keywords
Deep learning predicts DNA methylation regulatory variants in the human brain and elucidates the genetics of psychiatric disorders
Sign Up to like & getrecommendations! Published in 2022 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2206069119
Abstract: Significance Genetic association studies have identified widespread DNA methylation (DNAm) quantitative trait loci (mQTLs) that may illuminate causal genetic variations underlying human complex traits. However, due to extensive linkage disequilibrium (LD) of the genome, it… read more here.
Keywords: regulatory variants; dna methylation; human brain; deep learning ... See more keywords
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants.
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab189
Abstract: Understanding the functional consequence of noncoding variants is of great interest. Though genome-wide association studies or quantitative trait locus analyses have identified variants associated with traits or molecular phenotypes, most of them are located in… read more here.
Keywords: framework; statistical learning; regulatory variants; novel statistical ... See more keywords
RevUP, an online scoring system for regulatory variants implicated in rare diseases.
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac157
Abstract: SUMMARY To address the difficulty in assessing the implication of regulatory variants in diseases, a scoring scheme published by Van der Lee et al., 2020 allows the calculation of the Regulatory Variant Evidence score (RVE-score).… read more here.
Keywords: scoring system; regulatory variants; revup online; score ... See more keywords
Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty992
Abstract: Abstract Motivation Deciphering the functional roles of cis-regulatory variants is a critical challenge in genome analysis and interpretation. It has been hypothesized that altered transcription factor (TF) binding events are a central mechanism by which… read more here.
Keywords: binding events; regulatory variants; cis regulatory; gene expression ... See more keywords
Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance.
Sign Up to like & getrecommendations! Published in 2025 at "Genome research"
DOI: 10.1101/gr.280345.124
Abstract: Poultry egg production is shaped by the intertwined action of multiple physiological systems, greatly magnifying the complexity of its underlying genetic regulation. Although multitissue mapping of regulatory variants offers a powerful route to untangle this… read more here.
Keywords: egg; duck egg; regulatory variants; egg production ... See more keywords
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants
Sign Up to like & getrecommendations! Published in 2024 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2024.3374413
Abstract: Genome-wide association studies have shown that common genetic variants associated with complex diseases are mostly located in non-coding regions, which may not be causal. In addition, the limited number of validated non-coding functional variants makes… read more here.
Keywords: vector machine; support vector; regulatory variants; machine ... See more keywords
Regulatory variants in a novel distal enhancer regulate the expression of CYP3A4 and CYP3A5
Sign Up to like & getrecommendations! Published in 2022 at "Clinical and Translational Science"
DOI: 10.1111/cts.13398
Abstract: The cytochrome P450 3As (CYP3As) are abundantly expressed in the liver and metabolize many commonly prescribed medications. Their expression is highly variable between individuals with little known genetic cause. Despite extensive investigation, cis‐acting genetic elements… read more here.
Keywords: regulatory variants; expression; cyp3a4 cyp3a5; cyp3a4 ... See more keywords
Association of regulatory variants of dopamine β-hydroxylase with cognition and tardive dyskinesia in schizophrenia subjects
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Psychopharmacology"
DOI: 10.1177/0269881119895539
Abstract: Background: Dopamine-β-hydroxylase (DBH, EC 1.14.17.1), which converts dopamine to norepinephrine, is a candidate gene in neuropsychiatric diseases. Aim: To assess the effect of regulatory variants in DBH on schizophrenia and its endophenotypes –cognition and tardive… read more here.
Keywords: association; regulatory variants; tardive dyskinesia; cognition ... See more keywords
Systematic identification of regulatory variants associated with cancer risk
Sign Up to like & getrecommendations! Published in 2017 at "Genome Biology"
DOI: 10.1186/s13059-017-1322-z
Abstract: BackgroundMost cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to assess their functional impacts. To systematically identify the SNPs that affect gene expression by modulating… read more here.
Keywords: risk; cancer risk; regulatory variants; cancer ... See more keywords
Mapping regulatory variants controlling gene expression in drought response and tolerance in maize
Sign Up to like & getrecommendations! Published in 2020 at "Genome Biology"
DOI: 10.1186/s13059-020-02069-1
Abstract: Background Gene expression is a key determinant of cellular response. Natural variation in gene expression bridges genetic variation to phenotypic alteration. Identification of the regulatory variants controlling the gene expression in response to drought, a… read more here.
Keywords: drought; response; gene expression; regulatory variants ... See more keywords