Filters








12,403 Hits in 8.0 sec

FROM BINDING MOTIFS IN CHIP-SEQ DATA TO IMPROVED MODELS OF TRANSCRIPTION FACTOR BINDING SITES

IVAN KULAKOVSKIY, VICTOR LEVITSKY, DMITRY OSHCHEPKOV, LEONID BRYZGALOV, ILYA VORONTSOV, VSEVOLOD MAKEEV
2013 Journal of Bioinformatics and Computational Biology  
detect binding sites in ChIP-Seq data at a single base pair resolution.  ...  The wet-lab workflow is often supported by downstream computational analysis including construction of models of nucleotide sequences of transcription factor binding sites in DNA, which can be used to  ...  From Binding Motifs in ChIP-Seq Data to Improved TFBS Models Results and Discussion We have applied the strategy described in Methods to analyze three ChIP-Seq datasets and to estimate TFBS model quality  ... 
doi:10.1142/s0219720013400040 pmid:23427986 fatcat:wwnzqgzftfhlvclsdweyvy36je

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

Yuchun Guo, Shaun Mahony, David K. Gifford, Stein Aerts
2012 PLoS Computational Biology  
GEM's adaptive learning of binding-event read distributions allows it to further improve upon previous methods for processing ChIP-Seq and ChIP-exo data to yield unsurpassed spatial resolution and discovery  ...  GEM analysis of 63 transcription factors in 214 ENCODE human ChIP-Seq experiments recovers more known factor motifs than other contemporary methods, and discovers six new motifs for factors with unknown  ...  Edwards for suggestions on statistical testing methods for pairwise factor spatial binding constraints, Pouya Kheradpour for initial evaluation of motif discovery performances on ENCODE data, Tahin Syed  ... 
doi:10.1371/journal.pcbi.1002638 pmid:22912568 pmcid:PMC3415389 fatcat:j5i3dtuspnfzjdl7przpyv6y3y

Bayesian Markov models improve the prediction of binding motifs beyond first order without overfitting [article]

Wanwan Ge, Markus Meier, Christian Roth, Johannes Soeding
2020 bioRxiv   pre-print
Transcription factors regulate gene expression by binding to specific DNA motifs.  ...  However, they are more prone to overfit the data and to learn patterns merely correlated with rather than directly involved in transcription factor binding.  ...  and Ruoshi Zhang for discussions, and the genomics research community for sharing their data.  ... 
doi:10.1101/2020.07.12.197053 fatcat:arkcqvzd7vbjficotdeb6vxmfa

Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors [chapter]

Kenzie D. MacIsaac, Ernest Fraenkel
2010 Msphere  
Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome.  ...  In this chapter we review the tools, workflow, and common pitfalls of such analyses, and recommend strategies for effective motif discovery from these data.  ...  In this chapter we discuss tools and techniques for obtaining transcription factor binding specificity estimates from ChIP-chip and ChIP-seq data and for performing the downstream analyses that allows  ... 
doi:10.1007/978-1-60761-854-6_11 pmid:20827592 pmcid:PMC3922641 fatcat:u4e3puf5p5av3fcxb27rl6ltei

Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility

Sheng Liu, Cristina Zibetti, Jun Wan, Guohua Wang, Seth Blackshaw, Jiang Qian
2017 BMC Bioinformatics  
Computational prediction of transcription factor (TF) binding sites in different cell types is challenging.  ...  Furthermore, ChIP-Seq analysis was used to determine genome-wide binding sites for a range of different TFs in multiple cell types.  ...  Availability of data and materials TF motifs, Dnase-Seq, and ChIP-Seq data used are listed in Additional file 1.  ... 
doi:10.1186/s12859-017-1769-7 pmid:28750606 pmcid:PMC5530957 fatcat:i4gm4bbv4fa53dba6bokuzkb4m

Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites [article]

Henry E Pratt, Gregory R Andrews, Nishigandha Phalke, Michael J Purcaro, Arjan G van der Velde, Jill E Moore, Zhiping Weng
2021 biorxiv/medrxiv   pre-print
The binding specificities of these factors have been profiled both in vitro, using techniques such as HT-SELEX, and in vivo, using techniques including ChIP-seq.  ...  We previously developed Factorbook, a TF-centric database of annotations, motifs, and integrative analyses based on ChIP-seq data from Phase II of the ENCODE Project.  ...  DNase I protection hold even for motifs present in rDHSs but not ChIP-seq peaks, supporting the idea that at least a subset of these motifs are true transcription factor binding sites which would be identified  ... 
doi:10.1101/2021.10.11.463518 fatcat:qs5mfzelkvfaddaqazygddfsna

Base-pair resolution detection of transcription factor binding site by deep deconvolutional network [article]

Sirajul Salekin, Jianqiu (Michelle) Zhang, Yufei Huang
2018 bioRxiv   pre-print
We have also demonstrated the usefulness of DeepSNR in the regulatory analysis of TFBS as well as in improving the TFBS prediction specificity using ChIP-seq data.  ...  Transcription factor (TF) binds to the promoter region of a gene to control gene expres-sion.  ...  Conflict of Interest: none declared.  ... 
doi:10.1101/254508 fatcat:aobq7kz7hbdklnc3avpfo3y5xy

Base-pair resolution detection of transcription factor binding site by deep deconvolutional network

Sirajul Salekin, Jianqiu Michelle Zhang, Yufei Huang, John Hancock
2018 Bioinformatics  
We have also demonstrated the usefulness of DeepSNR in the regulatory analysis of TFBS as well as in improving the TFBS prediction specificity using ChIP-seq data.  ...  Motivation: Transcription factor (TF) binds to the promoter region of a gene to control gene expression.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bty383 pmid:29757349 fatcat:57llsjy4yng4jbm7q4jymrq4hu

Evaluating tools for transcription factor binding site prediction

Narayan Jayaram, Daniel Usvyat, Andrew C. R. Martin
2016 BMC Bioinformatics  
Binding of transcription factors to transcription factor binding sites (TFBSs) is key to the mediation of transcriptional regulation.  ...  Conclusions: Selection of the best-performing tools for generating PWMs from ChIP-Seq data and for scanning PWMs against DNA has the potential to improve prediction of precise transcription factor binding  ...  The set also contains data for 12 transcription factors with binding data in the ENCODE-ChIP-Seq data which come from a total of 149 genes ('PAZAR-E').  ... 
doi:10.1186/s12859-016-1298-9 pmid:27806697 fatcat:ncwrmqgcczaizhwvmjyfqnmiby

Bayesian Markov models improve the prediction of binding motifs beyond first order

Wanwan Ge, Markus Meier, Christian Roth, Johannes Söding
2021 NAR Genomics and Bioinformatics  
Transcription factors (TFs) regulate gene expression by binding to specific DNA motifs.  ...  We tested it with state-of-the-art motif discovery tools on a large collection of ChIP-seq and HT-SELEX datasets.  ...  and Ruoshi Zhang for discussions, and the genomics research community for sharing their data.  ... 
doi:10.1093/nargab/lqab026 pmid:33928244 pmcid:PMC8057495 fatcat:ki7o4kwzhneh7k3w7h4u2q4xem

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

Stephen A. Ramsey, Theo A. Knijnenburg, Kathleen A. Kennedy, Daniel E. Zak, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Aaron E. Lampano, Vladimir Litvak, Garnet Navarro, Tetyana Stolyar, Alan Aderem (+1 others)
2010 Computer applications in the biosciences : CABIOS  
This document contains supplementary information for the article Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites, including supplementary methods  ...  The resulting sequences were used to generate the TF binding site motif scanning feature, the GC content feature, and the nucleosome occupancy prediction score feature for the TF binding site prediction  ...  S1.6.1 Motivation Preliminary analysis of ChIP-Seq data for TFs and histone acetylation in murine macrophages revealed that transcription factor binding sites appear to be concentrated at local minima  ... 
doi:10.1093/bioinformatics/btq405 pmid:20663846 pmcid:PMC2922897 fatcat:qwg5yngzljf2fi2ooowutdvgke

Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information

Martin Nettling, Hendrik Treutler, Jesus Cerquides, Ivo Grosse
2016 BMC Genomics  
ChIP-seq has become the major technology to uncover genomic regions containing those binding sites, but motifs predicted by traditional computational approaches using these data are distorted by a ubiquitous  ...  Transcriptional gene regulation is a fundamental process in nature, and the experimental and computational investigation of DNA binding motifs and their binding sites is a prerequisite for elucidating  ...  Data The data used in this work originate from human ChIPseq data of the five human transcription factors CTCF, GABP, NRSF, SRF, and STAT1, where the ChIP-seq data for GABP and SRF published in [10]  ... 
doi:10.1186/s12864-016-2682-6 pmid:27165633 pmcid:PMC4862171 fatcat:kki2xgensnbsdiswk66m6pwbdy

DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

Myong-Hee Sung, Michael J. Guertin, Songjoon Baek, Gordon L. Hager
2014 Molecular Cell  
However, this model conflicts with previous reports of many TFs exchanging with specific binding sites in living cells on a time scale of seconds.  ...  Moreover, the nuclease cleavage profile within a footprint originates from the DNA sequence in the factor binding site, rather than from the protein occupying specific nucleotides.  ...  Acknowledgments Extensive use was made of the NIH Biowulf cluster, a GNU/Linux parallel processing system for computational analysis; we acknowledge the NIH Helix Systems Staff for management of this system  ... 
doi:10.1016/j.molcel.2014.08.016 pmid:25242143 pmcid:PMC4272573 fatcat:z555jgoc6nhyxcfdzikvim5w6y

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs

Morten Beck Rye, Pål Sætrom, Finn Drabløs
2010 Nucleic Acids Research  
Second, none of the programs returned peakregions that corresponded to the actual resolution in ChIP-seq data.  ...  Chromatin immunoprecipitation (ChIP) followed by high throughput sequencing (ChIP-seq) is rapidly becoming the method of choice for discovering cell-specific transcription factor binding locations genome  ...  Data sets The three ChIP-seq data sets used in this study were downloaded from the UCSC collection of ChIP-seq data.  ... 
doi:10.1093/nar/gkq1187 pmid:21113027 pmcid:PMC3045577 fatcat:uac4dpuu6neophypemq4uqjqti

The Role of Genome Accessibility in Transcription Factor Binding in Bacteria

Antonio L. C. Gomes, Harris H. Wang, Teresa M. Przytycka
2016 PLoS Computational Biology  
Furthermore, ChIP-seq data often poorly correlate with in vitro measurements or predicted motifs, highlighting that binding affinity alone is insufficient to explain transcription factor (TF)-binding in  ...  However, the biological insights generated from ChIP-seq analysis have been limited to predictions of binding sites and cooperative interactions.  ...  Acknowledgments We thank Nathan Johns for insightful feedback and members of the Wang lab for their support.  ... 
doi:10.1371/journal.pcbi.1004891 pmid:27104615 pmcid:PMC4841574 fatcat:lt64qyzvrzcblnttbzu2hrkqhm
« Previous Showing results 1 — 15 out of 12,403 results