Cargando…

Differential motif enrichment analysis of paired ChIP-seq experiments

BACKGROUND: Motif enrichment analysis of transcription factor ChIP-seq data can help identify transcription factors that cooperate or compete. Previously, little attention has been given to comparative motif enrichment analysis of pairs of ChIP-seq experiments, where the binding of the same transcri...

Descripción completa

Detalles Bibliográficos
Autores principales:	Lesluyes, Tom, Johnson, James, Machanick, Philip, Bailey, Timothy L
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2014
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167127/ https://www.ncbi.nlm.nih.gov/pubmed/25179504 http://dx.doi.org/10.1186/1471-2164-15-752

Ejemplares similares

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

Inferring direct DNA binding from ChIP-seq
por: Bailey, Timothy L., et al.
Publicado: (2012)

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data
por: Wu, Qian, et al.
Publicado: (2015)

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

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

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

Limitations and possibilities of low cell number ChIP-seq
por: Gilfillan, Gregor D, et al.
Publicado: (2012)

Shape-based peak identification for ChIP-Seq
por: Hower, Valerie, et al.
Publicado: (2011)

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
por: Qin, Zhaohui S, et al.
Publicado: (2010)

Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application
por: Zhong, Jian, et al.
Publicado: (2017)

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
por: McLeay, Robert C, et al.
Publicado: (2010)

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

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

Epigenomic profiling of archived FFPE tissues by enhanced PAT-ChIP (EPAT-ChIP) technology
por: Amatori, Stefano, et al.
Publicado: (2018)

Inferring transcription factor complexes from ChIP-seq data
por: Whitington, Tom, et al.
Publicado: (2011)

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

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

Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq
por: Busby, Michele, et al.
Publicado: (2016)

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

The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
por: Kornacker, Karl, et al.
Publicado: (2012)

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets
por: Schweikert, Gabriele, et al.
Publicado: (2013)

RACS: rapid analysis of ChIP-Seq data for contig based genomes
por: Saettone, Alejandro, et al.
Publicado: (2019)

ChIP-less analysis of chromatin states
por: Su, Zhangli, 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)

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

lobChIP: from cells to sequencing ready ChIP libraries in a single day
por: Wallerman, Ola, et al.
Publicado: (2015)

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
por: Lefrançois, Philippe, et al.
Publicado: (2009)

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
por: Nix, David A, et al.
Publicado: (2008)

Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq
por: Zhong, Jian, et al.
Publicado: (2019)

SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis
por: Zhao, Dejian, et al.
Publicado: (2018)

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

ChIP on Chip: surprising results are often artifacts
por: Waldminghaus, Torsten, et al.
Publicado: (2010)

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

Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data
por: Goi, Chin Lui, et al.
Publicado: (2013)

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

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

T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data
por: Almeida da Paz, Michelle, et al.
Publicado: (2022)

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

Cannot write session to /tmp/vufind_sessions/sess_ljje561rk2dugthjfp7u703v3c