Cargando…

Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells

BACKGROUND: To facilitate deciphering underlying transcriptional regulatory circuits in mouse embryonic stem (ES) cells, recent ChIP-seq data provided genome-wide binding locations of several key transcription factors (TFs); meanwhile, existing efforts profiled gene expression in ES cells and in the...

Descripción completa

Detalles Bibliográficos
Autores principales:	Chen, Gong, Zhou, Qing
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265564/ https://www.ncbi.nlm.nih.gov/pubmed/22011333 http://dx.doi.org/10.1186/1471-2164-12-515

Ejemplares similares

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

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

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

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

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
por: Qin, Jing, et al.
Publicado: (2011)

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

Identifying causal regulatory SNPs in ChIP-seq enhancers
por: Huang, Di, et al.
Publicado: (2015)

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)

Combining multiple ChIP-seq peak detection systems using combinatorial fusion
por: Schweikert, Christina, et al.
Publicado: (2012)

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

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)

An Optimized Protocol for ChIP-Seq from Human Embryonic Stem Cell Cultures
por: Sullivan, Adrienne E., et al.
Publicado: (2020)

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)

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq
por: Ma, Shaoqian, et al.
Publicado: (2020)

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

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)

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

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

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)

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

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism
por: Muhammad, Isiaka Ibrahim, et al.
Publicado: (2019)

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

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

ChIPulate: A comprehensive ChIP-seq simulation pipeline
por: Datta, Vishaka, et al.
Publicado: (2019)

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

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

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

Widespread Misinterpretable ChIP-seq Bias in Yeast
por: Park, Daechan, et al.
Publicado: (2013)

In Silico Pooling of ChIP-seq Control Experiments
por: Sun, Guannan, et al.
Publicado: (2014)

jChIP: a graphical environment for exploratory ChIP-Seq data analysis
por: Chojnowski, Krzysztof, et al.
Publicado: (2014)

Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets
por: Teng, Li, et al.
Publicado: (2014)

FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets
por: Zhang, Shaoqiang, et al.
Publicado: (2019)

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

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
por: Ather, Syed Hussain, et al.
Publicado: (2020)

Detection of Regulatory SNPs in Human Genome Using ChIP-seq ENCODE Data
por: Bryzgalov, Leonid O., et al.
Publicado: (2013)

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

Cannot write session to /tmp/vufind_sessions/sess_hac05jipa7s2ui2tl2v9091q53