Cargando…

HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency

MOTIVATION: Transcription factor (TF) binds to conservative DNA binding sites in different cellular environments and development stages by physical interaction with interdependent nucleotides. However, systematic computational characterization of the relationship between higher-order nucleotide depe...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wang, Zixuan, Xiong, Shuwen, Yu, Yun, Zhou, Jiliu, Zhang, Yongqing
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Original Paper
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10191609/ https://www.ncbi.nlm.nih.gov/pubmed/37140548 http://dx.doi.org/10.1093/bioinformatics/btad299

Ejemplares similares

Uncovering the Relationship between Tissue-Specific TF-DNA Binding and Chromatin Features through a Transformer-Based Model
por: Zhang, Yongqing, et al.
Publicado: (2022)

Deciphering the Nucleotide and RNA Binding Selectivity of the Mayaro Virus Macro Domain
por: Tsika, Aikaterini C., et al.
Publicado: (2019)

An integrated study to decipher immunosuppressive cellular communication in the PDAC environment
por: AVŞAR, Gülben, et al.
Publicado: (2023)

Synthesis of the Thomsen-Friedenreich-antigen (TF-antigen) and binding of Galectin-3 to TF-antigen presenting neo-glycoproteins
por: Hoffmann, Marius, et al.
Publicado: (2020)

Fine-Resolution Mapping of TF Binding and Chromatin Interactions
por: Gutin, Jenia, et al.
Publicado: (2018)

Inferring TF activation order in time series scRNA-Seq studies
por: Lin, Chieh, et al.
Publicado: (2020)

Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
por: Kang, Yiming, et al.
Publicado: (2020)

Age, dose, and binding to TfR on blood cells influence brain delivery of a TfR-transported antibody
por: Faresjö, Rebecca, et al.
Publicado: (2023)

Representing higher-order dependencies in networks
por: Xu, Jian, et al.
Publicado: (2016)

Radiation hardness of lead glasses TF1 and TF101
por: Kobayashi, M, et al.
Publicado: (1993)

TF-COMB – Discovering grammar of transcription factor binding sites
por: Bentsen, Mette, et al.
Publicado: (2022)

Second-Order Regression-Based MR Image Upsampling
por: Hu, Jing, et al.
Publicado: (2017)

Revealing eRNA interactions: TF dependency and convergent cooperativity
por: Lee, Seungha Alisa, et al.
Publicado: (2023)

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
por: Kheradpour, Pouya, et al.
Publicado: (2014)

Higher-order corrections to the $\Lambda$ binding energy in nuclear matter
por: Ranft, Gisela
Publicado: (1966)

Fractional-order quantum particle swarm optimization
por: Xu, Lai, et al.
Publicado: (2019)

Expression of flTF and asTF splice variants in various cell strains and tissues
por: Pan, Lili, et al.
Publicado: (2019)

Time Course of Priming Effect of TF Inducers on Synergistic TF Expression and Intra-Cellular Gap Formation of Human Vascular Endothelial Cells via the Extrinsic Coagulation Cascade
por: Matsubara, Daiki, et al.
Publicado: (2023)

Proteostasis Environment Shapes Higher-Order Epistasis Operating on Antibiotic Resistance
por: Guerrero, Rafael F., et al.
Publicado: (2019)

Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP‐TF and determination of its transcriptional effect
por: Xie, Meng, et al.
Publicado: (2020)

MetaSEM: Gene Regulatory Network Inference from Single-Cell RNA Data by Meta-Learning
por: Zhang, Yongqing, et al.
Publicado: (2023)

Deciphering the Function of Neurexins at Cellular Junctions
por: Littleton, J. Troy, et al.
Publicado: (1997)

Itemanalyse der Kurzformen des Tinnitusfragebogens: Mini-TF-12 und Mini-TF-15
por: Brueggemann, Petra, et al.
Publicado: (2023)

Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
por: Nicolaï, Adrien, et al.
Publicado: (2013)

Anarchic centromeres: deciphering order from apparent chaos()
por: Catania, Sandra, et al.
Publicado: (2014)

Temperature dependent Higher Order Modes (HOM) in the SRS cavities
por: McIntosh, P A, et al.
Publicado: (1996)

Research on User Behavior Based on Higher-Order Dependency Network
por: Qian, Liwei, et al.
Publicado: (2023)

The mineralocorticoid receptor forms higher order oligomers upon DNA binding
por: Fettweis, Gregory, et al.
Publicado: (2023)

Iron-loaded transferrin (Tf) is detrimental whereas iron-free Tf confers protection against brain ischemia by modifying blood Tf saturation and subsequent neuronal damage
por: DeGregorio-Rocasolano, Nuria, et al.
Publicado: (2017)

eRNA co-expression network uncovers TF dependency and convergent cooperativity
por: Lee, Seungha Alisa, et al.
Publicado: (2023)

CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria
por: Kılıç, Sefa, et al.
Publicado: (2014)

Deciphering MET‐dependent modulation of global cellular responses to DNA damage by quantitative phosphoproteomics
por: Bensimon, Ariel, et al.
Publicado: (2020)

Transferrin receptor (TfR) trafficking determines brain uptake of TfR antibody affinity variants
por: Bien-Ly, Nga, et al.
Publicado: (2014)

Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data
por: Yang, Chia-Chun, et al.
Publicado: (2017)

Higher-order computability
por: Longley, John, et al.
Publicado: (2015)

Higher Order Derivatives
por: Mukhopadhyay, Satya
Publicado: (2012)

Biozyme TF, tratamiento foliar : información técnica
Publicado: (1988)

Diffusion-Weighted Images Superresolution Using High-Order SVD
por: Wu, Xi, et al.
Publicado: (2016)

DNA replication timing and higher-order nuclear organization determine single nucleotide substitution patterns in cancer genomes
por: Liu, Lin, et al.
Publicado: (2013)

Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
por: van Eijk, Patrick, et al.
Publicado: (2019)

Cannot write session to /tmp/vufind_sessions/sess_cvag6qddvadmi3ja6tt9nbb388