Cargando…

Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles

Most of the position weight matrix (PWM) based bioinformatics methods developed to predict transcription factor binding sites (TFBS) assume each nucleotide in the sequence motif contributes independently to the interaction between protein and DNA sequence, usually producing high false positive predi...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bi, Yingtao, Kim, Hyunsoo, Gupta, Ravi, Davuluri, Ramana V.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Public Library of Science 2011
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166302/ https://www.ncbi.nlm.nih.gov/pubmed/21912677 http://dx.doi.org/10.1371/journal.pone.0024210

Ejemplares similares

IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data
por: Kim, Hyunsoo, et al.
Publicado: (2011)

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
por: Bi, Yingtao, et al.
Publicado: (2013)

Isoform level expression profiles provide better cancer signatures than gene level expression profiles
por: Zhang, ZhongFa, et al.
Publicado: (2013)

Evaluation of data discretization methods to derive platform independent isoform expression signatures for multi-class tumor subtyping
por: Jung, Segun, et al.
Publicado: (2015)

Occupancy Classification of Position Weight Matrix-Inferred Transcription Factor Binding Sites
por: Wright, Hollis, et al.
Publicado: (2011)

Dinucleotide Weight Matrices for Predicting Transcription Factor Binding Sites: Generalizing the Position Weight Matrix
por: Siddharthan, Rahul
Publicado: (2010)

Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms
por: Dapas, Matthew, et al.
Publicado: (2017)

Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis
por: Shilpi, Arunima, et al.
Publicado: (2017)

Assessment of Algorithms for Inferring Positional Weight Matrix Motifs of Transcription Factor Binding Sites Using Protein Binding Microarray Data
por: Orenstein, Yaron, et al.
Publicado: (2012)

Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites
por: Nandi, Soumyadeep, et al.
Publicado: (2012)

Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes
por: Pal, Sharmistha, et al.
Publicado: (2014)

Identification and validation of regulatory SNPs that modulate transcription factor chromatin binding and gene expression in prostate cancer
por: Jin, Hong-Jian, et al.
Publicado: (2016)

CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation
por: Plasschaert, Robert N., et al.
Publicado: (2014)

CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation
por: Plasschaert, Robert N., et al.
Publicado: (2014)

Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline
por: Stong, Nicholas, et al.
Publicado: (2014)

Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1)
por: Lu, Fang, et al.
Publicado: (2010)

Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia
por: Glass, Carolyn, et al.
Publicado: (2013)

Positional distribution of human transcription factor binding sites
por: Koudritsky, Mark, et al.
Publicado: (2008)

VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees
por: Grau, Jan, et al.
Publicado: (2006)

Stabilization of HIF-1α and HIF-2α, up-regulation of MYCC and accumulation of stabilized p53 constitute hallmarks of CNS-PNET animal model
por: Malchenko, Sergey, et al.
Publicado: (2017)

Distinct mechanisms control genome recognition by p53 at its target genes linked to different cell fates
por: Farkas, Marina, et al.
Publicado: (2021)

Optimized Position Weight Matrices in Prediction of Novel Putative Binding Sites for Transcription Factors in the Drosophila melanogaster Genome
por: Morozov, Vyacheslav Y., et al.
Publicado: (2013)

MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data
por: Gupta, Ravi, et al.
Publicado: (2011)

Prediction of Nucleosome Positioning Based on Transcription Factor Binding Sites
por: Yi, Xianfu, et al.
Publicado: (2010)

Positional distribution of transcription factor binding sites in Arabidopsis thaliana
por: Yu, Chun-Ping, et al.
Publicado: (2016)

A Graphical Modelling Approach to the Dissection of Highly Correlated Transcription Factor Binding Site Profiles
por: Stojnic, Robert, et al.
Publicado: (2012)

Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes
por: Liu, Xianpeng, et al.
Publicado: (2017)

Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices
por: Oh, Young Min, et al.
Publicado: (2012)

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data
por: Gupta, Ravi, et al.
Publicado: (2010)

CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data
por: Keleş, Sündüz, et al.
Publicado: (2008)

Position specific variation in the rate of evolution in transcription factor binding sites
por: Moses, Alan M, et al.
Publicado: (2003)

Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites
por: Gershenzon, Naum I., et al.
Publicado: (2005)

P-Match: transcription factor binding site search by combining patterns and weight matrices
por: Chekmenev, D. S., et al.
Publicado: (2005)

Protein Kinase A Activation Enhances β-Catenin Transcriptional Activity through Nuclear Localization to PML Bodies
por: Zhang, Mei, et al.
Publicado: (2014)

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
por: Price, Morgan N., et al.
Publicado: (2009)

Effect of positional dependence and alignment strategy on modeling transcription factor binding sites
por: Quader, Saad, et al.
Publicado: (2012)

Deep multi-omics integration by learning correlation-maximizing representation identifies prognostically stratified cancer subtypes
por: Ji, Yanrong, et al.
Publicado: (2023)

A Systems Biology Approach to Transcription Factor Binding Site Prediction
por: Zhou, Xiang, et al.
Publicado: (2010)

Reliable scaling of position weight matrices for binding strength comparisons between transcription factors
por: Ma, Xiaoyan, et al.
Publicado: (2015)

AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
por: Davuluri, Ramana V, et al.
Publicado: (2003)

Cannot write session to /tmp/vufind_sessions/sess_qgfv2fr1g8fjte8f495tf4cjls