Cargando…

Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data

We compared positional weight matrix-based prediction methods for transcription factor (TF) binding sites using selected fraction of ChIP-seq data with the help of partial AUC measure (limited to false positive rate 0.1, that is the most relevant for the application of the TF search in the genome sc...

Descripción completa

Detalles Bibliográficos
Autores principales:	Kondrakhin, Yu., Valeev, T., Sharipov, R., Yevshin, I., Kolpakov, F., Kel, A.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Elsevier 2016
Materias:	Regular Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988505/ https://www.ncbi.nlm.nih.gov/pubmed/29900118 http://dx.doi.org/10.1016/j.euprot.2016.09.001

Ejemplares similares

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments
por: Yevshin, Ivan, et al.
Publicado: (2017)

GTRD: a database on gene transcription regulation—2019 update
por: Yevshin, Ivan, et al.
Publicado: (2019)

Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data
por: Sharipov, Ruslan N., et al.
Publicado: (2020)

GTRD: an integrated view of transcription regulation
por: Kolmykov, Semyon, et al.
Publicado: (2020)

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data
por: Kolpakov, Fedor, et al.
Publicado: (2019)

Population size estimation for quality control of ChIP-Seq datasets
por: Kolmykov, Semyon K., et al.
Publicado: (2019)

BioUML—towards a universal research platform
por: Kolpakov, Fedor, et al.
Publicado: (2022)

CYCLONET—an integrated database on cell cycle regulation and carcinogenesis
por: Kolpakov, Fedor, et al.
Publicado: (2007)

Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data
por: Vorontsov, Ilya E., et al.
Publicado: (2018)

Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer
por: Kel, Alexander, et al.
Publicado: (2019)

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
por: Kulakovskiy, Ivan V, et al.
Publicado: (2018)

Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3
por: Boyarskikh, Ulyana, et al.
Publicado: (2018)

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome
por: Patel, Arjun, et al.
Publicado: (2023)

Protein Interaction Networks Link Schizophrenia Risk Loci to Synaptic Function
por: Schwarz, Emanuel, et al.
Publicado: (2016)

Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways
por: Kutumova, Elena, et al.
Publicado: (2013)

Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer
por: Kel, Alexander E., et al.
Publicado: (2016)

Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies
por: Alamanova, Denitsa, et al.
Publicado: (2010)

Thoroughly Calibrated Modular Agent-Based Model of the Human Cardiovascular and Renal Systems for Blood Pressure Regulation in Health and Disease
por: Kutumova, Elena, et al.
Publicado: (2021)

Mathematical modeling of antihypertensive therapy
por: Kutumova, Elena, et al.
Publicado: (2022)

Data on master regulators and transcription factor binding sites found by upstream analysis of multi-omics data on methotrexate resistance of colon cancer
por: Kel, Alexander E.
Publicado: (2016)

DNA polymerase delta interacting protein 3 facilitates the activation and maintenance of DNA damage checkpoint in response to replication stress
por: Zhang, Sufang, et al.
Publicado: (2022)

Corrigendum to “Data on master regulators and transcription factor binding sites found by upstream analysis of multi-omics data on methotrexate resistance of colon cancer” [Data Brief. 10 (2016) 499–504]
por: Kel, A.E.
Publicado: (2017)

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
por: Kulakovskiy, Ivan V., et al.
Publicado: (2016)

Identification and mapping of central pair proteins by proteomic analysis
por: Dai, Daniel, et al.
Publicado: (2020)

Multidomain protein structure prediction using information about residues interacting on multimeric protein interfaces
por: Matsuno, Shumpei, et al.
Publicado: (2020)

De novo derivation of proteomes from transcriptomes for transcript and protein identification
por: Evans, Vanessa C., et al.
Publicado: (2012)

Time, space, and disorder in the expanding proteome universe
por: Minde, David‐Paul, et al.
Publicado: (2017)

Mitoxantrone and ametantrone induce interstrand cross-links in DNA of tumour cells
por: Skladanowski, A, et al.
Publicado: (2000)

Filamin-A-interacting protein 1 (FILIP1) is a dual compartment protein linking myofibrils and microtubules during myogenic differentiation and upon mechanical stress
por: Grande, Valentina, et al.
Publicado: (2023)

Application of fluorescent-based technology detecting protein-protein interactions to monitor the binding of hepatitis B virus X protein to DNA-damage-binding protein 1
por: Omagari, Katsumi, et al.
Publicado: (2021)

Landscape of allele-specific transcription factor binding in the human genome
por: Abramov, Sergey, et al.
Publicado: (2021)

ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
por: Boytsov, Alexandr, et al.
Publicado: (2022)

Computational Prediction of Protein-Protein Interactions in Leishmania Predicted Proteomes
por: Rezende, Antonio M., et al.
Publicado: (2012)

proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data
por: Wang, Xiaojing, et al.
Publicado: (2016)

Hydrated electrons induce the formation of interstrand cross-links in DNA modified by cisplatin adducts
por: Behmand, B, et al.
Publicado: (2020)

Complementary Proteome and Transcriptome Profiling in Developing Grains of a Notched-Belly Rice Mutant Reveals Key Pathways Involved in Chalkiness Formation
por: Lin, Zhaomiao, et al.
Publicado: (2017)

Connecting and linking neurocognitive, digital phenotyping, physiologic, psychophysical, neuroimaging, genomic, & sensor data with survey data
por: Knott, Charles E., et al.
Publicado: (2021)

Critical controllability in proteome-wide protein interaction network integrating transcriptome
por: Ishitsuka, Masayuki, et al.
Publicado: (2016)

Phototropin Interactions with SUMO Proteins
por: Łabuz, Justyna, et al.
Publicado: (2021)

Integrating Genotypic Data With Transcriptomic and Proteomic Data
por: Shields, Denis C., et al.
Publicado: (2002)

Cannot write session to /tmp/vufind_sessions/sess_5lgirpn3v6jcshl81i7cvitq48