Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors

Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors

Transcriptional factors (TFs) bind in a combinatorial fashion to specify the on-and-off states of genes in a complex and redundant regulatory network. Here, the authors construct the transcription regulatory network in maize leaf using 104 TFs ChIP-seq data and train machine learning models to predi...

Полное описание

Библиографические подробности
Главные авторы:	Xiaoyu Tu, María Katherine Mejía-Guerra, Jose A. Valdes Franco, David Tzeng, Po-Yu Chu, Wei Shen, Yingying Wei, Xiuru Dai, Pinghua Li, Edward S. Buckler, Silin Zhong
Формат:	Статья
Язык:	English
Опубликовано:	Nature Portfolio 2020-10-01
Серии:	Nature Communications
Online-ссылка:	https://doi.org/10.1038/s41467-020-18832-8

Схожие документы

Author Correction: Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors
по: Xiaoyu Tu, и др.
Опубликовано: (2023-03-01)

Impact of artefact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.
по: Thomas Samuel Carroll, и др.
Опубликовано: (2014-04-01)

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
по: Karchenko Peter V, и др.
Опубликовано: (2011-02-01)

ChIP-Seq in Candida albicans
по: Sadri Znaidi, и др.
Опубликовано: (2014-06-01)

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
по: Pagès Hervé, и др.
Опубликовано: (2010-05-01)

Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping
по: Sachs Laurent, и др.
Опубликовано: (2009-12-01)

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data
по: Minucci Saverio, и др.
Опубликовано: (2011-10-01)

De novo ChIP-seq analysis
по: He, Xin, и др.
Опубликовано: (2015)

Normalization of ChIP-seq data with control
по: Liang Kun, и др.
Опубликовано: (2012-08-01)

Model-based Analysis of ChIP-Seq (MACS)
по: Zhang, Yong, и др.
Опубликовано: (2010)

ChIPseqR: analysis of ChIP-seq experiments
по: Helliwell Chris A, и др.
Опубликовано: (2011-01-01)

In silico pooling of ChIP-seq control experiments.
по: Guannan Sun, и др.
Опубликовано: (2014-01-01)

Shape-based peak identification for ChIP-Seq
по: Evans Steven N, и др.
Опубликовано: (2011-01-01)

ChIPulate: A comprehensive ChIP-seq simulation pipeline.
по: Vishaka Datta, и др.
Опубликовано: (2019-03-01)

A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques.
по: Haiyan Lei, и др.
Опубликовано: (2010-12-01)

About the variability, quality and reproducibility of ChIP-seq data
по: Hamzavi-Pinon Violaine, и др.
Опубликовано: (2016-06-01)

CSSQ: a ChIP-seq signal quantifier pipeline
по: Ashwath Kumar, и др.
Опубликовано: (2023-05-01)

An integrated ChIP-seq analysis platform with customizable workflows
по: Giannopoulou Eugenia G, и др.
Опубликовано: (2011-07-01)

BayesPeak: Bayesian analysis of ChIP-seq data
по: Stark Rory, и др.
Опубликовано: (2009-09-01)

Limitations and possibilities of low cell number ChIP-seq
по: Gilfillan Gregor D, и др.
Опубликовано: (2012-11-01)

Evaluation of algorithm performance in ChIP-seq peak detection.
по: Elizabeth G Wilbanks, и др.
Опубликовано: (2010-07-01)

Practical guidelines for the comprehensive analysis of ChIP-seq data.
по: Timothy Bailey, и др.
Опубликовано: (2013-01-01)

Identifying differential transcription factor binding in ChIP-seq
по: Dai-Ying eWu, и др.
Опубликовано: (2015-04-01)

Histone modification ChIP-seq on Arabidopsis thaliana Plantlets
по: Juan Ramirez-Prado, и др.
Опубликовано: (2021-11-01)

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome
по: David A. Orlando, и др.
Опубликовано: (2014-11-01)

aFARP-ChIP-seq, a convenient and reliable method for genome profiling in as few as 100 cells with a capability for multiplexing ChIP-seq
по: Wenbin Liu, и др.
Опубликовано: (2019-09-01)

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq
по: Shaoqian Ma, и др.
Опубликовано: (2020-10-01)

iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets
по: Wei Yingying, и др.
Опубликовано: (2012-11-01)

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
по: Kheradpour, Pouya, и др.
Опубликовано: (2013)

Large-Scale Quality Analysis of Published ChIP-seq Data
по: Kundaje, Anshul, и др.
Опубликовано: (2014)

peaksat: an R package for ChIP-seq peak saturation analysis
по: Joseph R Boyd, и др.
Опубликовано: (2023-01-01)

A Clustering Approach for Motif Discovery in ChIP-Seq Dataset
по: Chun-xiao Sun, и др.
Опубликовано: (2019-08-01)

A comparison of control samples for ChIP-seq of histone modifications
по: Christoffer eFlensburg, и др.
Опубликовано: (2014-09-01)

Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application
по: Jian Zhong, и др.
Опубликовано: (2017-12-01)

Q&A: ChIP-seq technologies and the study of gene regulation
по: Pott Sebastian, и др.
Опубликовано: (2010-05-01)

Population size estimation for quality control of ChIP-Seq datasets.
по: Semyon K Kolmykov, и др.
Опубликовано: (2019-01-01)

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data
по: Qian Wu, и др.
Опубликовано: (2015-01-01)

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data
по: Qian Wu, и др.
Опубликовано: (2015-01-01)

Quantitative ChIP-seq by Adding Spike-in from Another Species
по: Kongyan Niu, и др.
Опубликовано: (2018-08-01)

Effects of sheared chromatin length on ChIP-seq quality and sensitivity
по: Cheryl A Keller, и др.
Опубликовано: (2021-03-01)