Cargando…

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data

The ChIP-chip and ChIP-seq techniques enable genome-wide mapping of in vivo protein-DNA interactions and chromatin states. The cross-platform and between-laboratory variation poses a challenge to the comparison and integration of results from different ChIP experiments. We describe a novel method, M...

Descripción completa

Detalles Bibliográficos
Autores principales:	Chen, Yiwen, Meyer, Clifford A, Liu, Tao, Li, Wei, Liu, Jun S, Liu, Xiaole Shirley
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188793/ https://www.ncbi.nlm.nih.gov/pubmed/21284836 http://dx.doi.org/10.1186/gb-2011-12-2-r11

Ejemplares similares

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

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

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

Model-based Analysis of ChIP-Seq (MACS)
por: Zhang, Yong, et al.
Publicado: (2008)

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

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

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

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)

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

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

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

HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples
por: Chen, Haojie, et al.
Publicado: (2022)

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

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)

Impact of sequencing depth in ChIP-seq experiments
por: Jung, Youngsook L., et al.
Publicado: (2014)

ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles
por: Chen, Xi, et al.
Publicado: (2016)

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

A ChIP on the shoulder? Chromatin immunoprecipitation and validation strategies for ChIP antibodies
por: Wardle, Fiona C., et al.
Publicado: (2015)

ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
por: Oki, Shinya, et al.
Publicado: (2018)

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

SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPs
por: Anand, Shankara, et al.
Publicado: (2019)

Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET
por: Mathur, Divya, et al.
Publicado: (2008)

An integrated ChIP-seq analysis platform with customizable workflows
por: Giannopoulou, Eugenia G, et al.
Publicado: (2011)

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

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data
por: Yang, Chia-Chun, et al.
Publicado: (2016)

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

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

To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq
por: Xu, Jinrui, et al.
Publicado: (2020)

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

Fast genomic μChIP-chip from 1,000 cells
por: Dahl, John Arne, et al.
Publicado: (2009)

MAnorm2 for quantitatively comparing groups of ChIP-seq samples
por: Tu, Shiqi, et al.
Publicado: (2021)

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
por: Ambrosini, Giovanna, et al.
Publicado: (2016)

SpikChIP: a novel computational methodology to compare multiple ChIP-seq using spike-in chromatin
por: Blanco, Enrique, et al.
Publicado: (2021)

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

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq
por: Liu, Peng, et al.
Publicado: (2016)

Analyzing ChIP-chip Data Using Bioconductor
por: Toedling, Joern, et al.
Publicado: (2008)

Normalization and experimental design for ChIP-chip data
por: Peng, Shouyong, et al.
Publicado: (2007)

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

Cannot write session to /tmp/vufind_sessions/sess_mq8m3fu8l16phonndh0nmnh52c