An interactive web application for the dissemination of human systems immunology data

Cate Speake, Scott Presnell, Kelly Domico, Brad Zeitner, Anna Bjork, David Anderson, Michael J. Mason, Elizabeth Whalen, Olivia Vargas, Dimitry Popov, Darawan Rinchai, Noemie Jourde-Chiche, Laurent Chiche, Charlie Quinn, Damien J. Chaussabel

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Background: Systems immunology approaches have proven invaluable in translational research settings. The current rate at which large-scale datasets are generated presents unique challenges and opportunities. Mining aggregates of these datasets could accelerate the pace of discovery, but new solutions are needed to integrate the heterogeneous data types with the contextual information that is necessary for interpretation. In addition, enabling tools and technologies facilitating investigators' interaction with large-scale datasets must be developed in order to promote insight and foster knowledge discovery. Methods: State of the art application programming was employed to develop an interactive web application for browsing and visualizing large and complex datasets. A collection of human immune transcriptome datasets were loaded alongside contextual information about the samples. Results: We provide a resource enabling interactive query and navigation of transcriptome datasets relevant to human immunology research. Detailed information about studies and samples are displayed dynamically; if desired the associated data can be downloaded. Custom interactive visualizations of the data can be shared via email or social media. This application can be used to browse context-rich systems-scale data within and across systems immunology studies. This resource is publicly available online at [Gene Expression Browser Landing Page (https://gxb.benaroyaresearch.org/dm3/landing.gsp)]. The source code is also available openly [Gene Expression Browser Source Code (https://github.com/BenaroyaResearch/gxbrowser)]. Conclusions: We have developed a data browsing and visualization application capable of navigating increasingly large and complex datasets generated in the context of immunological studies. This intuitive tool ensures that, whether taken individually or as a whole, such datasets generated at great effort and expense remain interpretable and a ready source of insight for years to come.

Original languageEnglish
Article number196
JournalJournal of Translational Medicine
Volume13
Issue number1
DOIs
Publication statusPublished - 19 Jun 2015
Externally publishedYes

Fingerprint

Immunology
Allergy and Immunology
Information Systems
Landing
Gene expression
Visualization
Electronic mail
Transcriptome
Data mining
Navigation
Social Media
Gene Expression
Translational Medical Research
Datasets
Research Personnel
Technology

Keywords

  • Bioinformatics
  • Immunology
  • Software
  • Transcriptomics

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

An interactive web application for the dissemination of human systems immunology data. / Speake, Cate; Presnell, Scott; Domico, Kelly; Zeitner, Brad; Bjork, Anna; Anderson, David; Mason, Michael J.; Whalen, Elizabeth; Vargas, Olivia; Popov, Dimitry; Rinchai, Darawan; Jourde-Chiche, Noemie; Chiche, Laurent; Quinn, Charlie; Chaussabel, Damien J.

In: Journal of Translational Medicine, Vol. 13, No. 1, 196, 19.06.2015.

Research output: Contribution to journalArticle

Speake, C, Presnell, S, Domico, K, Zeitner, B, Bjork, A, Anderson, D, Mason, MJ, Whalen, E, Vargas, O, Popov, D, Rinchai, D, Jourde-Chiche, N, Chiche, L, Quinn, C & Chaussabel, DJ 2015, 'An interactive web application for the dissemination of human systems immunology data', Journal of Translational Medicine, vol. 13, no. 1, 196. https://doi.org/10.1186/s12967-015-0541-x
Speake, Cate ; Presnell, Scott ; Domico, Kelly ; Zeitner, Brad ; Bjork, Anna ; Anderson, David ; Mason, Michael J. ; Whalen, Elizabeth ; Vargas, Olivia ; Popov, Dimitry ; Rinchai, Darawan ; Jourde-Chiche, Noemie ; Chiche, Laurent ; Quinn, Charlie ; Chaussabel, Damien J. / An interactive web application for the dissemination of human systems immunology data. In: Journal of Translational Medicine. 2015 ; Vol. 13, No. 1.
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