Cargando…

PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks

RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. Howe...

Descripción completa

Detalles Bibliográficos
Autores principales:	Lin, Jianan, Zhang, Yuping, Frankel, Wayne N., Ouyang, Zhengqing
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2019
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6716675/ https://www.ncbi.nlm.nih.gov/pubmed/31425505 http://dx.doi.org/10.1371/journal.pcbi.1007227

Ejemplares similares

PRAS40 signaling in tumor
por: Lv, Dan, et al.
Publicado: (2017)

Peakhood: individual site context extraction for CLIP-seq peak regions
por: Uhl, Michael, et al.
Publicado: (2021)

LISA: Accurate reconstruction of cell trajectory and pseudo-time for massive single cell RNA-seq data
por: Chen, Yang, et al.
Publicado: (2019)

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data
por: Fukunaga, Tsukasa, et al.
Publicado: (2014)

Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB
por: Lin, Jianan, et al.
Publicado: (2020)

PRAS40 hyperexpression promotes hepatocarcinogenesis
por: Qi, Zhaolai, et al.
Publicado: (2020)

Deciphering the role of RNA structure in translation efficiency
por: Lin, Jianan, et al.
Publicado: (2022)

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
por: Drewe-Boss, Philipp, et al.
Publicado: (2018)

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
por: Krakau, Sabrina, et al.
Publicado: (2017)

Discovery of Protein–lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets
por: Li, Jun-Hao, et al.
Publicado: (2015)

CLIPdb: a CLIP-seq database for protein-RNA interactions
por: Yang, Yu-Cheng T, et al.
Publicado: (2015)

Seq and CLIP through the miRNA world
por: Mittal, Nitish, et al.
Publicado: (2014)

SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins
por: Chen, Fan, et al.
Publicado: (2020)

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

Widespread autogenous mRNA–protein interactions detected by CLIP-seq
por: Kapral, Thomas H, et al.
Publicado: (2022)

A new graph-based clustering method with application to single-cell RNA-seq data from human pancreatic islets
por: Wu, Hao, et al.
Publicado: (2021)

mTOR/PRAS40 interaction: Hypertrophy or proliferation
por: Völkers, Mirko, et al.
Publicado: (2013)

Robust transcriptome-wide discovery of RNA binding protein binding sites with enhanced CLIP (eCLIP)
por: Van Nostrand, Eric L., et al.
Publicado: (2016)

Bloom Syndrome Protein Activates AKT and PRAS40 in Prostate Cancer Cells
por: Chen, Kun, et al.
Publicado: (2019)

Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding
por: Serra, Fabrizio, et al.
Publicado: (2021)

Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq
por: Biancon, Giulia, et al.
Publicado: (2022)

DeepCLIP: predicting the effect of mutations on protein–RNA binding with deep learning
por: Grønning, Alexander Gulliver Bjørnholt, et al.
Publicado: (2020)

From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data
por: Bottini, Silvia, et al.
Publicado: (2017)

Identification of CELF1 RNA targets by CLIP-seq in human HeLa cells
por: Le Tonquèze, Olivier, et al.
Publicado: (2016)

Recent computational developments on CLIP-seq data analysis and microRNA targeting implications
por: Bottini, Silvia, et al.
Publicado: (2017)

A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data
por: Li, Shuya, et al.
Publicado: (2017)

TGFβ signaling-induced miRNA participates in autophagic regulation by targeting PRAS40 in mesenchymal subtype of glioblastoma
por: Xie, Yingbin, et al.
Publicado: (2020)

CLIP-based prediction of mammalian microRNA binding sites
por: Liu, Chaochun, et al.
Publicado: (2013)

A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data
por: Wang, Tao, et al.
Publicado: (2014)

dCLIP: a computational approach for comparative CLIP-seq analyses
por: Wang, Tao, et al.
Publicado: (2014)

PRAS40 and PRR5-Like Protein Are New mTOR Interactors that Regulate Apoptosis
por: Thedieck, Kathrin, et al.
Publicado: (2007)

Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes
por: Kurotani, Atsushi, et al.
Publicado: (2017)

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
por: Ouyang, Zhengqing, et al.
Publicado: (2013)

High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq
por: Gumienny, Rafal, et al.
Publicado: (2017)

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis
por: Chen, Beibei, et al.
Publicado: (2014)

Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis
por: Heyl, Florian, et al.
Publicado: (2020)

Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP
por: Lorenz, Daniel A., et al.
Publicado: (2022)

Saturation analysis of ChIP-seq data for reproducible identification of binding peaks
por: Hansen, Peter, et al.
Publicado: (2015)

Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
por: Gomes, Antonio L.C., et al.
Publicado: (2014)

PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information
por: Wu, Hao, et al.
Publicado: (2014)

Cannot write session to /tmp/vufind_sessions/sess_ubds6bf8fsq99n5g6bm1renbcr