A curated transcriptome dataset collection to investigate the immunobiology of HIV infection

Jana Blazkova, Sabri Boughorbel, Scott Presnell, Charlie Quinn, Damien J. Chaussabel

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Compendia of large-scale datasets available in public repositories provide an opportunity to identify and fill current gaps in biomedical knowledge. But first, these data need to be readily accessible to research investigators for interpretation. Here, we make available a collection of transcriptome datasets relevant to HIV infection. A total of 2717 unique transcriptional profiles distributed among 34 datasets were identified, retrieved from the NCBI Gene Expression Omnibus (GEO), and loaded in a custom web application, the Gene Expression Browser (GXB), designed for interactive query and visualization of integrated large-scale data. Multiple sample groupings and rank lists were created to facilitate dataset query and interpretation via this interface. Web links to customized graphical views can be generated by users and subsequently inserted in manuscripts reporting novel findings, such as discovery notes. The tool also enables browsing of a single gene across projects, which can provide new perspectives on the role of a given molecule across biological systems. This curated dataset collection is available at: http://hiv.gxbsidra.org/dm3/geneBrowser/list.

Original languageEnglish
Article number327
Pages (from-to)1
Number of pages1
JournalF1000Research
Volume5
DOIs
Publication statusPublished - 2016

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Transcriptome
Gene expression
HIV Infections
Biological systems
Visualization
Genes
Molecules
Gene Expression
Manuscripts
Research Personnel
Datasets
Research

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

Cite this

A curated transcriptome dataset collection to investigate the immunobiology of HIV infection. / Blazkova, Jana; Boughorbel, Sabri; Presnell, Scott; Quinn, Charlie; Chaussabel, Damien J.

In: F1000Research, Vol. 5, 327, 2016, p. 1.

Research output: Contribution to journalArticle

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