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DNA-Protein Interactions

Overview of attention for book
Cover of 'DNA-Protein Interactions'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 Electrophoretic Mobility Shift Assay Using Radiolabeled DNA Probes
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    Chapter 2 In Vitro DNase I Footprinting
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    Chapter 3 DNA-Protein Interactions
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    Chapter 4 In Cellulo DNA Analysis: LMPCR Footprinting.
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    Chapter 5 Southwestern Blotting Assay
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    Chapter 6 Single-Molecule Approaches for the Characterization of Riboswitch Folding Mechanisms
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    Chapter 7 Probing of Nascent Riboswitch Transcripts
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    Chapter 8 DNA-Protein Interactions
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    Chapter 9 Precise Identification of Genome-Wide Transcription Start Sites in Bacteria by 5'-Rapid Amplification of cDNA Ends (5'-RACE).
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    Chapter 10 Analysis of DNA Supercoiling Induced by DNA-Protein Interactions.
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    Chapter 11 Precise Identification of DNA-Binding Proteins Genomic Location by Exonuclease Coupled Chromatin Immunoprecipitation (ChIP-exo).
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    Chapter 12 The Cruciform DNA Mobility Shift Assay: A Tool to Study Proteins That Recognize Bent DNA.
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    Chapter 13 Individual and Sequential Chromatin Immunoprecipitation Protocols.
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    Chapter 14 Chromatin Endogenous Cleavage (ChEC) as a Method to Quantify Protein Interaction with Genomic DNA in Saccharomyces cerevisiae.
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    Chapter 15 Selection and Validation of Spacer Sequences for CRISPR-Cas9 Genome Editing and Transcription Regulation in Bacteria.
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    Chapter 16 Detection of Short-Range DNA Interactions in Mammalian Cells Using High-Resolution Circular Chromosome Conformation Capture Coupled to Deep Sequencing.
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    Chapter 17 Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq).
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    Chapter 18 Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler.
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    Chapter 19 Circular Dichroism for the Analysis of Protein–DNA Interactions
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    Chapter 20 Quantitative Investigation of Protein–Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance
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    Chapter 21 Identification of Nucleic Acid High Affinity Binding Sequences of Proteins by SELEX
Attention for Chapter 18: Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler.
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Chapter title
Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler.
Chapter number 18
Book title
DNA-Protein Interactions
Published in
Methods in molecular biology, January 2015
DOI 10.1007/978-1-4939-2877-4_18
Pubmed ID
26404157
Book ISBNs
978-1-4939-2876-7, 978-1-4939-2877-4
Authors

Brunelle, Mylène, Coulombe, Charles, Poitras, Christian, Robert, Marc-Antoine, Markovits, Alexei Nordell, Robert, François, Jacques, Pierre-Étienne, Mylène Brunelle, Charles Coulombe, Christian Poitras, Marc-Antoine Robert, Alexei Nordell Markovits, François Robert, Pierre-Étienne Jacques

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.

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X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
 Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 7 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 7 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 4 57%
Professor 1 14%
Student > Bachelor 1 14%
Professor > Associate Professor 1 14%
Readers by discipline Count As %
Computer Science 3 43%
Business, Management and Accounting 1 14%
Biochemistry, Genetics and Molecular Biology 1 14%
Agricultural and Biological Sciences 1 14%
Nursing and Health Professions 1 14%
Other 0 0%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 26 September 2015.
All research outputs
#20,292,660
of 22,829,083 outputs
Outputs from Methods in molecular biology
#9,916
of 13,125 outputs
Outputs of similar age
#295,850
of 353,131 outputs
Outputs of similar age from Methods in molecular biology
#636
of 997 outputs
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So far Altmetric has tracked 13,125 research outputs from this source. They receive a mean Attention Score of 3.4. This one is in the 1st percentile – i.e., 1% of its peers scored the same or lower than it.
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