ArticleNucleic acids research2014
VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.Molecular cell · 2021Article
- Crucial role of Salmonella genomic island 1 master activator in the parasitism of IncC plasmids.Nucleic acids research · 2021Article
- Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.RNA biology · 2021Article
- Integrative characterization of the near-minimal bacterium Mesoplasma florum.Molecular systems biology · 2020Article
- Article
- Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription.The EMBO journal · 2019Article
- Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast.Nature communications · 2018Article
- Global inhibition of transcription causes an increase in histone H2A.Z incorporation within gene bodies.Nucleic acids research · 2017Article
- Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes.Nucleic acids research · 2017Article
- Live-cell analysis of DNA methylation during sexual reproduction in Arabidopsis reveals context and sex-specific dynamics controlled by noncanonical RdDM.Genes & development · 2017Article
- Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo.Molecular cell · 2016Article
- An interactive environment for agile analysis and visualization of ChIP-sequencing data.Nature structural & molecular biology · 2016Article
- Recruitment of Saccharomyces cerevisiae Cmr1/Ydl156w to Coding Regions Promotes Transcription Genome Wide.PloS one · 2016Article
- Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III.Nature communications · 2015Article
- The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations.Molecular cell · 2015Article
- Histone deacetylases and phosphorylated polymerase II C-terminal domain recruit Spt6 for cotranscriptional histone reassembly.Molecular and cellular biology · 2014Article
- The master activator of IncA/C conjugative plasmids stimulates genomic islands and multidrug resistance dissemination.PLoS genetics · 2014Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The analysis of genomic data such as ChIP-Seq usually involves representing the signal intensity level over genes or other genetic features. This is often illustrated as a curve (representing the aggregate profile of a group of genes) or as a heatmap (representing individual genes). However, no specific resource dedicated to easily generating such profiles is currently available. We therefore built the versatile aggregate profiler (VAP), designed to be used by experimental and computational biologists to generate profiles of genomic datasets over groups of regions of interest, using either an absolute or a relative method. Graphical representation of the results is automatically generated, and subgrouping can be performed easily, based on the orientation of the flanking annotations. The outputs include statistical measures to facilitate comparisons between groups or datasets. We show that, through its intuitive design and flexibility, VAP can help avoid misinterpretations of genomics data. VAP is highly efficient and designed to run on laptop computers by using a memory footprint control, but can also be easily compiled and run on servers. VAP is accessible at http://lab-jacques.recherche.usherbrooke.ca/vap/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.