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

Abstract

BackgroundSystems 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.MethodsState 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.ResultsWe 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)].ConclusionsWe 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.

Increased abundance of ADAM9 transcripts in the blood is associated with tissue damage

“…Next, the initial observation was validated and further extended by examining profiles of the gene of interest, ADAM9, across a large number of independent publically available transcriptome datasets. The completion of these tasks was aided by a custom data browsing application loaded with a curated compendium of 172 datasets relevant to human immunology sourced from the National Center for Biotechnology Information’s (NCBI) Gene Expression Omnibus (GEO) ( https://gxb.benaroyaresearch.org/dm3/landing.gsp) 17 . Briefly, ADAM9 transcript was identified as a potential early stage discovery while browsing RNA-sequencing profiles of blood leukocyte populations ( https://gxb.benaroyaresearch.org/dm3/geneBrowser/show/396), with the genes being ranked in alphabetical order.…”

“…We employed a resource that is described in details 17 and is available publicly: https://gxb.benaroyaresearch.org/dm3/landing.gsp. Briefly: we have assembled and curated a collection of 172 datasets that are relevant to human immunology, representing a total of 12,886 unique transcriptome profiles.…”

“…The custom software interface provides the user with a means to easily navigate and filter the compendium of available datasets ( https://gxb.benaroyaresearch.org/dm3/geneBrowser/list) 17, 18 . Datasets of interest can be quickly identified either by filtering on criteria from pre-defined lists on the left or by entering a query term in the search box at the top of the dataset navigation page, we also provided the GXB tutorial in YouTube video; https://www.youtube.com/playlist?list=PLtx3tvfIzJ9XkRKUz6ISEJpAhqKyuiCiD.…”

­A curated transcriptomic dataset collection relevant to embryonic development associated with in vitro fertilization in healthy individuals and patients with polycystic ovary syndrome

“…After curation, each dataset was downloaded from the Gene Expression Omnibus of the National Center for Biotechnology Information website (NCBI GEO) using the SOFT file format, and was then uploaded, along with its study information and samples available, to the Gene Expression Browser, version 1.2 (GXB; http://ivf.gxbsidra.org/dm3/geneBrowser/list), an interactive web-based application developed at the Benaroya Research Institute (Seattle, WA, USA), hosted on the Amazon Web Services cloud ( https://github.com/BenaroyaResearch/gxbrowser) ( https://aws.amazon.com) 21 . In GXB, we grouped the samples according to the expected future interpretation and comparison of study results.…”

“…A web tutorial for GXB is available online: http://ivf.gxbsidra.org/dm3/tutorials.gsp#gxbtut and is briefly reproduced here so that readers can use this article as a standalone resource 21, 22 : “datasets of interest can be quickly identified either by filtering criteria from pre-defined lists shown on the left side of the GXB dataset navigation window, or by entering a query term in the search box located at its left top portion. Clicking on one of the studies listed in the dataset navigation window opens a viewer, which is designed to provide interactive browsing and graphic representations of the large-scale data in an interpretable format.…”