Cargando…

PromoterPredict: sequence-based modelling of Escherichia coli σ(70) promoter strength yields logarithmic dependence between promoter strength and sequence

We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ(70) factor of RNA polymerase. σ(70) promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both ti...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bharanikumar, Ramit, Premkumar, Keshav Aditya R., Palaniappan, Ashok
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2018
Materias:	Bioinformatics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6228582/ https://www.ncbi.nlm.nih.gov/pubmed/30425888 http://dx.doi.org/10.7717/peerj.5862

Ejemplares similares

Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy
por: Premkumar, Keshav Aditya R., et al.
Publicado: (2020)

Escherichia coli σ(70) senses sequence and conformation of the promoter spacer region
por: Singh, Shivani S., et al.
Publicado: (2011)

Anatomy of Escherichia coli σ(70) promoters
por: Shultzaberger, Ryan K., et al.
Publicado: (2007)

Predicting the strength of UP-elements and full-length E. coli σ(E) promoters
por: Rhodius, Virgil A., et al.
Publicado: (2012)

BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins
por: Basu, Sankar, et al.
Publicado: (2021)

Identification and characterization of sequence signatures in the Bacillus subtilis promoter P(ylb) for tuning promoter strength
por: Xu, Jiangtao, et al.
Publicado: (2019)

Systematic dissection of σ(70) sequence diversity and function in bacteria
por: Park, Jimin, et al.
Publicado: (2021)

In vitro transcription profiling of the σ(S) subunit of bacterial RNA polymerase: re-definition of the σ(S) regulon and identification of σ(S)-specific promoter sequence elements
por: Maciąg, Anna, et al.
Publicado: (2011)

miR2Trait: an integrated resource for investigating miRNA-disease associations
por: Babu, Poornima, et al.
Publicado: (2022)

CESCProg: a compact prognostic model and nomogram for cervical cancer based on miRNA biomarkers
por: Muthamilselvan, Sangeetha, et al.
Publicado: (2023)

BrcaDx: precise identification of breast cancer from expression data using a minimal set of features
por: Muthamilselvan, Sangeetha, et al.
Publicado: (2023)

SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas
por: Coppens, Lucas, et al.
Publicado: (2020)

Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients
por: Belikov, Aleksey V., et al.
Publicado: (2022)

GABRP promotes CD44s-mediated gemcitabine resistance in pancreatic cancer
por: Chen, Chen, et al.
Publicado: (2022)

The Rhizobium etli σ(70) (SigA) factor recognizes a lax consensus promoter
por: Ramírez-Romero, Miguel A., et al.
Publicado: (2006)

Prolactin may serve as a regulator to promote vocal fold wound healing
por: Wang, Haizhou, et al.
Publicado: (2020)

Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend
por: Wei, Kai, et al.
Publicado: (2019)

TransPrise: a novel machine learning approach for eukaryotic promoter prediction
por: Pachganov, Stepan, et al.
Publicado: (2019)

TBX3 regulates the transcription of VEGFA to promote osteoblasts proliferation and microvascular regeneration
por: Wu, Lichuang, et al.
Publicado: (2022)

Modeling DNA-binding of Escherichia coli σ(70) exhibits a characteristic energy landscape around strong promoters
por: Weindl, Johanna, et al.
Publicado: (2007)

Escherichia coli σ(70) promoters allow expression rate control at the cellular level in genome-integrated expression systems
por: Schuller, Artur, et al.
Publicado: (2020)

Indexing labeled sequences
por: Rocher, Tatiana, et al.
Publicado: (2018)

LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression
por: Zhou, Wei, et al.
Publicado: (2020)

Comparison of machine learning and deep learning techniques in promoter prediction across diverse species
por: Bhandari, Nikita, et al.
Publicado: (2021)

BIRC5 promotes cancer progression and predicts prognosis in laryngeal squamous cell carcinoma
por: Wang, Nan, et al.
Publicado: (2022)

Expression and promoter analysis of MEP pathway enzyme-encoding genes in Pinus massoniana Lamb
por: Zhu, Peihuang, et al.
Publicado: (2022)

High expression of MAPK-14 promoting the death of chondrocytes is an important signal of osteoarthritis process
por: Deng, Zhiqin, et al.
Publicado: (2021)

A journey through the Corynebacterium pseudotuberculosis proteome promotes insights into its functional genome
por: Marques da Silva, Wanderson, et al.
Publicado: (2021)

The law of the iterated logarithm for LNQD sequences
por: Zhang, Yong
Publicado: (2018)

Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes
por: Huerta, Araceli M, et al.
Publicado: (2006)

Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships
por: Duarte-Velázquez, Isabel, et al.
Publicado: (2022)

Insight to Gene Expression From Promoter Libraries With the Machine Learning Workflow Exp2Ipynb
por: Liebal, Ulf W., et al.
Publicado: (2021)

FTH1 indicates poor prognosis and promotes metastasis in head and neck squamous cell carcinoma
por: Liao, Qingyun, et al.
Publicado: (2023)

CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classification
por: Peng, He
Publicado: (2020)

Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type
por: Liu, Yen-Yi, et al.
Publicado: (2021)

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions
por: Jia, Kejue, et al.
Publicado: (2023)

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data
por: Dzida, Tomasz, et al.
Publicado: (2017)

ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning
por: Malkowska, Maja, et al.
Publicado: (2018)

Dipeptidyl peptidase like 6 promoter methylation is a potential prognostic biomarker for pancreatic ductal adenocarcinoma
por: Zhao, Xin, et al.
Publicado: (2020)

NFIB promotes the migration and progression of kidney renal clear cell carcinoma by regulating PINK1 transcription
por: Wang, Ninghua, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_t0lr0jarggssgtl24sso511l7m