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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W485-93. doi: 10.1093/nar/gku302. Epub 2014 Apr 21.

VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery.

Author information

1
Département d'informatique, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada.
2
Institut de recherches cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.
3
Département d'informatique, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada.
4
Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada.
5
Institut de recherches cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada Département de médecine, Faculté de médecine, Université de Montréal, Montréal, Québec, H3T 1J4, Canada Pierre-Etienne.Jacques@USherbrooke.ca.
6
Département d'informatique, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada Pierre-Etienne.Jacques@USherbrooke.ca.

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/.

PMID:
24753414
PMCID:
PMC4086060
DOI:
10.1093/nar/gku302
[Indexed for MEDLINE]
Free PMC Article

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