Cargando…

Measuring similarities between transcription factor binding sites

BACKGROUND: Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites. RESULTS: We propose to identify and group simi...

Descripción completa

Detalles Bibliográficos
Autores principales:	Kielbasa, Szymon M, Gonze, Didier, Herzel, Hanspeter
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2005
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1261160/ https://www.ncbi.nlm.nih.gov/pubmed/16191190 http://dx.doi.org/10.1186/1471-2105-6-237

Ejemplares similares

Inferring combinatorial regulation of transcription in silico
por: Blüthgen, Nils, et al.
Publicado: (2005)

Jaccard index based similarity measure to compare transcription factor binding site models
por: Vorontsov, Ilya E, et al.
Publicado: (2013)

Predicting transcription factor binding sites using local over-representation and comparative genomics
por: Defrance, Matthieu, et al.
Publicado: (2006)

MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations
por: Keilwagen, Jens, et al.
Publicado: (2009)

xFITOM: a generic GUI tool to search for transcription factor binding sites
por: Bhargava, Nidhi, et al.
Publicado: (2010)

Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites
por: Hosseini, Parsa, et al.
Publicado: (2013)

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
por: Marinescu, Voichita D, et al.
Publicado: (2005)

Synchronization-Induced Rhythmicity of Circadian Oscillators in the Suprachiasmatic Nucleus
por: Bernard, Samuel, et al.
Publicado: (2007)

Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse
por: Steinhoff, Christine, et al.
Publicado: (2009)

DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites
por: Blom, Evert-Jan, et al.
Publicado: (2008)

CpG Deamination Creates Transcription Factor–Binding Sites with High Efficiency
por: Żemojtel, Tomasz, et al.
Publicado: (2011)

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks
por: Chen, Chen, et al.
Publicado: (2021)

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes
por: Hestand, Matthew S, et al.
Publicado: (2008)

HuSiDa—the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells
por: Truss, Matthias, et al.
Publicado: (2005)

Integrating omics datasets with the OmicsPLS package
por: Bouhaddani, Said el, et al.
Publicado: (2018)

Integrating binding and expression data to predict transcription factors combined function
por: Ahmed, Mahmoud, et al.
Publicado: (2020)

Regulation of Clock-Controlled Genes in Mammals
por: Bozek, Katarzyna, et al.
Publicado: (2009)

CLUSS: Clustering of protein sequences based on a new similarity measure
por: Kelil, Abdellali, et al.
Publicado: (2007)

FISim: A new similarity measure between transcription factor binding sites based on the fuzzy integral
por: Garcia, Fernando, et al.
Publicado: (2009)

Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach
por: Broin, Pilib Ó, et al.
Publicado: (2015)

SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions
por: Nishizaki, Sierra S., et al.
Publicado: (2022)

DOSim: An R package for similarity between diseases based on Disease Ontology
por: Li, Jiang, et al.
Publicado: (2011)

The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites
por: Cereto-Massagué, Adrià, et al.
Publicado: (2013)

The Transcription Factor Encyclopedia
por: Yusuf, Dimas, et al.
Publicado: (2012)

A tool for calculating binding-site residues on proteins from PDB structures
por: Hu, Jing, et al.
Publicado: (2009)

RBPsuite: RNA-protein binding sites prediction suite based on deep learning
por: Pan, Xiaoyong, et al.
Publicado: (2020)

GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products
por: Fröhlich, Holger, et al.
Publicado: (2007)

LIGSITE(csc): predicting ligand binding sites using the Connolly surface and degree of conservation
por: Huang, Bingding, et al.
Publicado: (2006)

Genome-wide prediction, display and refinement of binding sites with information theory-based models
por: Gadiraju, Sashidhar, et al.
Publicado: (2003)

NormiRazor: tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies
por: Grabia, Szymon, et al.
Publicado: (2020)

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins
por: Zhang, Jing, et al.
Publicado: (2020)

CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation
por: Wang, Liuyang, et al.
Publicado: (2015)

PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool
por: Dai, Xinbin, et al.
Publicado: (2013)

MODSIDE: a motif discovery pipeline and similarity detector
por: Tran, Ngoc Tam L., et al.
Publicado: (2018)

A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae
por: Wu, Wei-Sheng, et al.
Publicado: (2014)

Blazing Signature Filter: a library for fast pairwise similarity comparisons
por: Lee, Joon-Yong, et al.
Publicado: (2018)

EGN: a wizard for construction of gene and genome similarity networks
por: Halary, Sébastien, et al.
Publicado: (2013)

TFCat: the curated catalog of mouse and human transcription factors
por: Fulton, Debra L, et al.
Publicado: (2009)

Identification of transcription factor high accumulation DNA zones
por: Cascianelli, Silvia, et al.
Publicado: (2023)

P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure
por: Krivák, Radoslav, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_nsevb65l3i0bp8conq1nu6csfq