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Literature DB >> 26404157

Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler.

Mylène Brunelle¹, Charles Coulombe², Christian Poitras³, Marc-Antoine Robert¹, Alexei Nordell Markovits¹, François Robert^3,4, Pierre-Étienne Jacques^5,6,7.

Abstract

In the analysis of experimental data corresponding to the signal enrichment of chromatin features such as histone modifications throughout the genome, it is often useful to represent the signal over known regions of interest, such as genes, using aggregate or individual profiles. In the present chapter, we describe and explain the best practices on how to generate such profiles as well as other usages of the versatile aggregate profiler (VAP) tool (Coulombe et al., Nucleic Acids Res 42:W485-W493, 2014), with a particular focus on the new functionalities introduced in version 1.1.0 of VAP.

Keywords: Aggregate profiles; Average profiles; ChIP-Seq; Data analysis; Graphical representation; Heatmaps

Mesh：

Substances：
Chromatin

Year: 2015 PMID： 26404157 DOI： 10.1007/978-1-4939-2877-4_18

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

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Cited

8 in total

1. Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription.

Authors: Julieta Rivosecchi; Marc Larochelle; Camille Teste; Frédéric Grenier; Amélie Malapert; Emiliano P Ricci; Pascal Bernard; François Bachand; Vincent Vanoosthuyse
Journal: EMBO J Date: 2019-07-11 Impact factor: 11.598

2. Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo.

Authors: Célia Jeronimo; Marie-France Langelier; Alain R Bataille; John M Pascal; B Franklin Pugh; François Robert
Journal: Mol Cell Date: 2016-10-20 Impact factor: 17.970

3. FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.

Authors: Célia Jeronimo; Andrew Angel; Vu Q Nguyen; Jee Min Kim; Christian Poitras; Elie Lambert; Pierre Collin; Jane Mellor; Carl Wu; François Robert
Journal: Mol Cell Date: 2021-08-10 Impact factor: 19.328

4. Acetylation-Dependent Recruitment of the FACT Complex and Its Role in Regulating Pol II Occupancy Genome-Wide in Saccharomyces cerevisiae.

Authors: Rakesh Pathak; Priyanka Singh; Sudha Ananthakrishnan; Sarah Adamczyk; Olivia Schimmel; Chhabi K Govind
Journal: Genetics Date: 2018-04-25 Impact factor: 4.562

Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler.

1. Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription.

2. Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo.

3. FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.

4. Acetylation-Dependent Recruitment of the FACT Complex and Its Role in Regulating Pol II Occupancy Genome-Wide in Saccharomyces cerevisiae.

5. Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes.

6. SWI/SNF and RSC cooperate to reposition and evict promoter nucleosomes at highly expressed genes in yeast.

7. The deubiquitylase Ubp15 couples transcription to mRNA export.

8. Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast.