Cargando…

Predicting the impact of non-coding variants on DNA methylation

DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences o...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zeng, Haoyang, Gifford, David K.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2017
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499808/ https://www.ncbi.nlm.nih.gov/pubmed/28334830 http://dx.doi.org/10.1093/nar/gkx177

Ejemplares similares

regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants
por: Zhang, Shijie, et al.
Publicado: (2019)

Exploring functional variant discovery in non-coding regions with SInBaD
por: Lehmann, Kjong-Van, et al.
Publicado: (2013)

A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction
por: Guo, Yuchun, et al.
Publicado: (2018)

Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome
por: Dong, Shengcheng, et al.
Publicado: (2021)

DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants
por: Wang, Meng, et al.
Publicado: (2018)

Optimized high-throughput screening of non-coding variants identified from genome-wide association studies
por: Morova, Tunc, et al.
Publicado: (2022)

EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants
por: Parvandeh, Saeid, et al.
Publicado: (2022)

Direct detection of methylation in genomic DNA
por: Bart, A., et al.
Publicado: (2005)

Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation
por: Yegnasubramanian, Srinivasan, et al.
Publicado: (2006)

CoRAL: predicting non-coding RNAs from small RNA-sequencing data
por: Leung, Yuk Yee, et al.
Publicado: (2013)

Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA
por: Blackledge, Neil P., et al.
Publicado: (2012)

EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes
por: Santoni, Federico Andrea
Publicado: (2013)

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts
por: Sun, Liang, et al.
Publicado: (2013)

Fractal construction of constrained code words for DNA storage systems
por: Löchel, Hannah F, et al.
Publicado: (2021)

miRVaS: a tool to predict the impact of genetic variants on miRNAs
por: Cammaerts, Sophia, et al.
Publicado: (2016)

Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks
por: Guo, Xingli, et al.
Publicado: (2013)

IMHOTEP—a composite score integrating popular tools for predicting the functional consequences of non-synonymous sequence variants
por: Knecht, Carolin, et al.
Publicado: (2017)

Low-level processing of Illumina Infinium DNA Methylation BeadArrays
por: Triche, Timothy J., et al.
Publicado: (2013)

MSRE-PCR for analysis of gene-specific DNA methylation
por: Melnikov, Anatoliy A., et al.
Publicado: (2005)

BASiNET—BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification
por: Ito, Eric Augusto, et al.
Publicado: (2018)

DNA bar coding and pyrosequencing to analyze adverse events in therapeutic gene transfer
por: Wang, Gary P., et al.
Publicado: (2008)

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations
por: Hoffmann, Christian, et al.
Publicado: (2007)

Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization
por: Eklund, Aron C., et al.
Publicado: (2010)

A multidimensional platform for the purification of non-coding RNA species
por: Chionh, Yok Hian, et al.
Publicado: (2013)

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
por: Briggs, Adrian W., et al.
Publicado: (2010)

Identification of active regulatory regions from DNA methylation data
por: Burger, Lukas, et al.
Publicado: (2013)

Using long-read sequencing to detect imprinted DNA methylation
por: Gigante, Scott, et al.
Publicado: (2019)

IDR2D identifies reproducible genomic interactions
por: Krismer, Konstantin, et al.
Publicado: (2020)

spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer–promoter interactions
por: Hammelman, Jennifer, et al.
Publicado: (2022)

A synergistic DNA logic predicts genome-wide chromatin accessibility
por: Hashimoto, Tatsunori, et al.
Publicado: (2016)

Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease
por: Liu, Yibin, et al.
Publicado: (2017)

Control of carry-over contamination for PCR-based DNA methylation quantification using bisulfite treated DNA
por: Tetzner, Reimo, et al.
Publicado: (2007)

CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data
por: Li, Wenyuan, et al.
Publicado: (2018)

CPPred: coding potential prediction based on the global description of RNA sequence
por: Tong, Xiaoxue, et al.
Publicado: (2019)

R-Coffee: a method for multiple alignment of non-coding RNA
por: Wilm, Andreas, et al.
Publicado: (2008)

Novel insight into the non-coding repertoire through deep sequencing analysis
por: Isakov, Ofer, et al.
Publicado: (2012)

A multi-parametric flow cytometric assay to analyze DNA–protein interactions
por: Arbab, Mandana, et al.
Publicado: (2013)

A high-throughput DNA methylation analysis of a single cell
por: Kantlehner, Martin, et al.
Publicado: (2011)

Quantitative comparison of within-sample heterogeneity scores for DNA methylation data
por: Scherer, Michael, et al.
Publicado: (2020)

MethReg: estimating the regulatory potential of DNA methylation in gene transcription
por: Silva, Tiago C, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_nr1jga0kcrsol8brfmc7g1mjrb