ArticleJournal of translational medicine2015
An interactive web application for the dissemination of human systems immunology data.
Article in Journal of translational medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Machine learning-enabled prediction of prolonged length of stay in hospital after surgery for tuberculosis spondylitis patients with unbalanced data: a novel approach using explainable artificial intelligence (XAI).European journal of medical research · 2024Article
- Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker.F1000Research · 2022Article
- SysInflam HuDB, a Web Resource for Mining Human Blood Cells Transcriptomic Data Associated with Systemic Inflammatory Responses to Sepsis.Journal of immunology (Baltimore, Md. : 1950) · 2021Article
- Transcriptome and Literature Mining Highlight the Differential Expression of ERLIN1 in Immune Cells during Sepsis.Biology · 2021Article
- Annexin A3 in sepsis: novel perspectives from an exploration of public transcriptome data.Immunology · 2020Review
- A modular framework for the development of targeted Covid-19 blood transcript profiling panels.Journal of translational medicine · 2020Article
- A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination.F1000Research · 2019Article
- A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.Database : the journal of biological databases and curation · 2019Article
- A curated transcriptome dataset collection to investigate inborn errors of immunity.F1000Research · 2019Article
- Long-Chain Acyl-CoA Synthetase 1 Role in Sepsis and Immunity: Perspectives From a Parallel Review of Public Transcriptome Datasets and of the Literature.Frontiers in immunology · 2019Review
- 'Omics Approaches to Explore the Breast Cancer Landscape.Frontiers in cell and developmental biology · 2019Review
- Using 'collective omics data' for biomedical research training.Immunology · 2018Review
- Unveiling differentially expressed genes upon regulation of transcription factors in sepsis.3 Biotech · 2017Article
- Article
- A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification.F1000Research · 2017Article
- A curated transcriptome dataset collection to investigate the functional programming of human hematopoietic cells in early life.F1000Research · 2016Article
- A curated transcriptome dataset collection to investigate the development and differentiation of the human placenta and its associated pathologies.F1000Research · 2016Article
- A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research.F1000Research · 2016Article
- A compendium of monocyte transcriptome datasets to foster biomedical knowledge discovery.F1000Research · 2016Article
- A curated transcriptome dataset collection to investigate the immunobiology of HIV infection.F1000Research · 2016Article
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Authors and funding
15 authors.
Funding
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.
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