Cargando…

Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA

BACKGROUND: ChIP-seq provides a wealth of information on the approximate location of DNA-binding proteins genome-wide. It is known that the targeted motifs in most cases can be found at the peak centers. A high resolution mapping of ChIP-seq peaks could in principle allow the fine mapping of the pro...

Descripción completa

Detalles Bibliográficos
Autores principales:	Nagy, Gergely, Czipa, Erik, Steiner, László, Nagy, Tibor, Pongor, Sándor, Nagy, László, Barta, Endre
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2016
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4986361/ https://www.ncbi.nlm.nih.gov/pubmed/27526722 http://dx.doi.org/10.1186/s12864-016-2940-7

Ejemplares similares

ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them
por: Czipa, Erik, et al.
Publicado: (2020)

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
por: Ibn-Salem, Jonas, et al.
Publicado: (2019)

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data
por: Wu, George, et al.
Publicado: (2013)

DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
por: Sebestyén, Endre, et al.
Publicado: (2009)

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information
por: Ma, Xiaotu, et al.
Publicado: (2012)

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data
por: Carroll, Thomas S., et al.
Publicado: (2014)

Motif grammar: The basis of the language of gene expression
por: Nagy, Gergely, et al.
Publicado: (2020)

DREME: motif discovery in transcription factor ChIP-seq data
por: Bailey, Timothy L.
Publicado: (2011)

Differential motif enrichment analysis of paired ChIP-seq experiments
por: Lesluyes, Tom, et al.
Publicado: (2014)

A Clustering Approach for Motif Discovery in ChIP-Seq Dataset
por: Sun, Chun-xiao, et al.
Publicado: (2019)

Motif elucidation in ChIP-seq datasets with a knockout control
por: Denisko, Danielle, et al.
Publicado: (2023)

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
por: Thomas-Chollier, Morgane, et al.
Publicado: (2012)

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data
por: Chen, Yiwen, et al.
Publicado: (2011)

seqMINER: an integrated ChIP-seq data interpretation platform
por: Ye, Tao, et al.
Publicado: (2011)

An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data
por: Ji, Hongkai, et al.
Publicado: (2008)

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
por: Ho, Joshua WK, et al.
Publicado: (2011)

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
por: Zhu, Lihua J, et al.
Publicado: (2010)

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
por: Worsley Hunt, Rebecca, et al.
Publicado: (2014)

ChIP-Enrich: gene set enrichment testing for ChIP-seq data
por: Welch, Ryan P., et al.
Publicado: (2014)

ChIP-AP: an integrated analysis pipeline for unbiased ChIP-seq analysis
por: Suryatenggara, Jeremiah, et al.
Publicado: (2021)

PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets
por: Yu, Qiang, et al.
Publicado: (2016)

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data
por: Barozzi, Iros, et al.
Publicado: (2011)

Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping
por: Buisine, Nicolas, et al.
Publicado: (2009)

W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data
por: Lan, Xun, et al.
Publicado: (2011)

SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data
por: Ding, Jun, et al.
Publicado: (2014)

A Fast Cluster Motif Finding Algorithm for ChIP-Seq Data Sets
por: Zhang, Yipu, et al.
Publicado: (2015)

Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs
por: Berger, Severin, et al.
Publicado: (2019)

WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data
por: Zhang, Hongbo, et al.
Publicado: (2017)

Web-MCOT Server for Motif Co-Occurrence Search in ChIP-Seq Data
por: Levitsky, Victor G., et al.
Publicado: (2022)

MEME-ChIP: motif analysis of large DNA datasets
por: Machanick, Philip, et al.
Publicado: (2011)

Inferring transcriptional modules from ChIP-chip, motif and microarray data
por: Lemmens, Karen, et al.
Publicado: (2006)

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq
por: Guertin, Michael J, et al.
Publicado: (2018)

Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders
por: Uusküla-Reimand, Liis, et al.
Publicado: (2016)

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data
por: Tran, Ngoc Tam L, et al.
Publicado: (2014)

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking
por: Wu, George, et al.
Publicado: (2013)

ChIPseqR: analysis of ChIP-seq experiments
por: Humburg, Peter, et al.
Publicado: (2011)

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments
por: Zambelli, Federico, et al.
Publicado: (2013)

Normalization of ChIP-seq data with control
por: Liang, Kun, et al.
Publicado: (2012)

De novo ChIP-seq analysis
por: He, Xin, et al.
Publicado: (2015)

ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data
por: Wu, Song, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_sbh348j2rvgpd9btb9lnffgs0t