Cargando…

MTSplice predicts effects of genetic variants on tissue-specific splicing

We develop the free and open-source model Multi-tissue Splicing (MTSplice) to predict the effects of genetic variants on splicing of cassette exons in 56 human tissues. MTSplice combines MMSplice, which models constitutive regulatory sequences, with a new neural network that models tissue-specific r...

Descripción completa

Detalles Bibliográficos
Autores principales:	Cheng, Jun, Çelik, Muhammed Hasan, Kundaje, Anshul, Gagneur, Julien
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2021
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8011109/ https://www.ncbi.nlm.nih.gov/pubmed/33789710 http://dx.doi.org/10.1186/s13059-021-02273-7

Ejemplares similares

Publisher Correction: MTSplice predicts effects of genetic variants on tissue-specific splicing
por: Cheng, Jun, et al.
Publicado: (2021)

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing
por: Cheng, Jun, et al.
Publicado: (2019)

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding
por: Cochran, Kelly, et al.
Publicado: (2022)

Co-expression networks reveal the tissue-specific regulation of transcription and splicing
por: Saha, Ashis, et al.
Publicado: (2017)

Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications
por: Sullivan, Patricia J., et al.
Publicado: (2023)

Homolog-specific PCR primer design for profiling splice variants
por: Srivastava, Gyan Prakash, et al.
Publicado: (2011)

Linking disease associations with regulatory information in the human genome
por: Schaub, Marc A., et al.
Publicado: (2012)

RegVar: Tissue-specific Prioritization of Non-coding Regulatory Variants
por: Lu, Hao, et al.
Publicado: (2023)

Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing data sets
por: Evans, Perry, et al.
Publicado: (2019)

Modular decomposition of protein-protein interaction networks
por: Gagneur, Julien, et al.
Publicado: (2004)

ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease
por: Sangermano, Riccardo, et al.
Publicado: (2018)

Umap and Bismap: quantifying genome and methylome mappability
por: Karimzadeh, Mehran, et al.
Publicado: (2018)

CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping
por: Marinov, Georgi K., et al.
Publicado: (2023)

Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning
por: Horlacher, Marc, et al.
Publicado: (2023)

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data
por: Cmero, Marek, et al.
Publicado: (2021)

RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing
por: Cereda, Matteo, et al.
Publicado: (2014)

Predicting RNA splicing from DNA sequence using Pangolin
por: Zeng, Tony, et al.
Publicado: (2022)

Detection of aberrant splicing events in RNA-seq data using FRASER
por: Mertes, Christian, et al.
Publicado: (2021)

Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases
por: Louadi, Zakaria, et al.
Publicado: (2021)

Assessing conservation of alternative splicing with evolutionary splicing graphs
por: Zea, Diego Javier, et al.
Publicado: (2021)

A spotter’s guide to SNPtic exons: The common splice variants underlying some SNP–phenotype correlations
por: Keegan, Niall Patrick, et al.
Publicado: (2021)

SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays
por: Anton, Miguel A, et al.
Publicado: (2008)

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
por: Kundaje, Anshul, et al.
Publicado: (2012)

Human Splicing Finder: an online bioinformatics tool to predict splicing signals
por: Desmet, François-Olivier, et al.
Publicado: (2009)

sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression
por: He, Yuan, et al.
Publicado: (2020)

Author Correction: Detection of aberrant splicing events in RNA-seq data using FRASER
por: Mertes, Christian, et al.
Publicado: (2022)

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics
por: Avsec, Žiga, et al.
Publicado: (2019)

Screening for functional transcriptional and splicing regulatory variants with GenIE
por: Cooper, Sarah E, et al.
Publicado: (2020)

Allele-specific alternative splicing and its functional genetic variants in human tissues
por: Amoah, Kofi, et al.
Publicado: (2021)

Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency
por: Adamson, Scott I., et al.
Publicado: (2018)

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
por: Hoffmann, Steve, et al.
Publicado: (2014)

Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens
por: Bredthauer, Carl, et al.
Publicado: (2023)

A microarray configuration to quantify expression levels and relative abundance of splice variants
por: Fehlbaum, Pascale, et al.
Publicado: (2005)

CRISPR-SKIP: programmable gene splicing with single base editors
por: Gapinske, Michael, et al.
Publicado: (2018)

Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints
por: Schwessinger, Ron, et al.
Publicado: (2017)

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

SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples
por: Yalamanchili, Hari Krishna, et al.
Publicado: (2014)

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data
por: Rogers, Mark F, et al.
Publicado: (2012)

Rare variants regulate expression of nearby individual genes in multiple tissues
por: Li, Jiajin, et al.
Publicado: (2021)

Simultaneous characterization of sense and antisense genomic processes by the double-stranded hidden Markov model
por: Glas, Julia, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_5qtef41l7rsmhl2bb1f5qt730i