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Exploring and visualizing multidimensional data in translational research platforms.

ABSTRACT: The unprecedented advances in technology and scientific research over the past few years have provided the scientific community with new and more complex forms of data. Large data sets collected from single groups or cross-institution consortiums containing hundreds of omic and clinical variables corresponding to thousands of patients are becoming increasingly commonplace in the research setting. Before any core analyses are performed, visualization often plays a key role in the initial phases of research, especially for projects where no initial hypotheses are dominant. Proper visualization of data at a high level facilitates researcher's abilities to find trends, identify outliers and perform quality checks. In addition, research has uncovered the important role of visualization in data analysis and its implied benefits facilitating our understanding of disease and ultimately improving patient care. In this work, we present a review of the current landscape of existing tools designed to facilitate the visualization of multidimensional data in translational research platforms. Specifically, we reviewed the biomedical literature for translational platforms allowing the visualization and exploration of clinical and omics data, and identified 11 platforms: cBioPortal, interactive genomics patient stratification explorer, Igloo-Plot, The Georgetown Database of Cancer Plus, tranSMART, an unnamed data-cube-based model supporting heterogeneous data, Papilio, Caleydo Domino, Qlucore Omics, Oracle Health Sciences Translational Research Center and OmicsOffice® powered by TIBCO Spotfire. In a health sector continuously witnessing an increase in data from multifarious sources, visualization tools used to better grasp these data will grow in their importance, and we believe our work will be useful in guiding investigators in similar situations.

SUBMITTER: Dunn W

PROVIDER: S-EPMC5862238 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Exploring and visualizing multidimensional data in translational research platforms.

Dunn William W Burgun Anita A Krebs Marie-Odile MO Rance Bastien B

Briefings in bioinformatics 20171101 6

The unprecedented advances in technology and scientific research over the past few years have provided the scientific community with new and more complex forms of data. Large data sets collected from single groups or cross-institution consortiums containing hundreds of omic and clinical variables corresponding to thousands of patients are becoming increasingly commonplace in the research setting. Before any core analyses are performed, visualization often plays a key role in the initial phases o ...[more]

PMID: 27585944

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Project description:Improvements in next-generation sequencing technologies have resulted in dramatically reduced sequencing costs. This has led to an explosion of '-seq'-based methods, of which RNA sequencing (RNA-seq) for generating transcriptomic data is the most popular. By analysing global patterns of gene expression in organs/tissues/cells of interest or in response to chemical or environmental perturbations, researchers can better understand an organism's biology. Tools designed to work with large RNA-seq data sets enable analyses and visualizations to help generate hypotheses about a gene's function. We present here a user-friendly RNA-seq data exploration tool, called the 'eFP-Seq Browser', that shows the read map coverage of a gene of interest in each of the samples along with 'electronic fluorescent pictographic' (eFP) images that serve as visual representations of expression levels. The tool also summarizes the details of each RNA-seq experiment, providing links to archival databases and publications. It automatically computes the reads per kilobase per million reads mapped expression-level summaries and point biserial correlation scores to sort the samples based on a gene's expression level or by how dissimilar the read map profile is from a gene splice variant, to quickly identify samples with the strongest expression level or where alternative splicing might be occurring. Links to the Integrated Genome Browser desktop visualization tool allow researchers to visualize and explore the details of RNA-seq alignments summarized in eFP-Seq Browser as coverage graphs. We present four cases of use of the eFP-Seq Browser for ABI3, SR34, SR45a and U2AF65B, where we examine expression levels and identify alternative splicing. The URL for the browser is https://bar.utoronto.ca/eFP-Seq_Browser/. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. Tool is at https://bar.utoronto.ca/eFP-Seq_Browser/; RNA-seq data at https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/ and https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/Klepikova/. Code is available at https://github.com/BioAnalyticResource/eFP-Seq-Browser.

Project description:BackgroundThe recent surge in clinical and nonclinical health-related data has been accompanied by a concomitant increase in personal health data (PHD) research across multiple disciplines such as medicine, computer science, and management. There is now a need to synthesize the dynamic knowledge of PHD in various disciplines to spot potential research hotspots.ObjectiveThe aim of this study was to reveal the knowledge evolutionary trends in PHD and detect potential research hotspots using bibliometric analysis.MethodsWe collected 8281 articles published between 2009 and 2018 from the Web of Science database. The knowledge evolution analysis (KEA) framework was used to analyze the evolution of PHD research. The KEA framework is a bibliometric approach that is based on 3 knowledge networks: reference co-citation, keyword co-occurrence, and discipline co-occurrence.ResultsThe findings show that the focus of PHD research has evolved from medicine centric to technology centric to human centric since 2009. The most active PHD knowledge cluster is developing knowledge resources and allocating scarce resources. The field of computer science, especially the topic of artificial intelligence (AI), has been the focal point of recent empirical studies on PHD. Topics related to psychology and human factors (eg, attitude, satisfaction, education) are also receiving more attention.ConclusionsOur analysis shows that PHD research has the potential to provide value-based health care in the future. All stakeholders should be educated about AI technology to promote value generation through PHD. Moreover, technology developers and health care institutions should consider human factors to facilitate the effective adoption of PHD-related technology. These findings indicate opportunities for interdisciplinary cooperation in several PHD research areas: (1) AI applications for PHD; (2) regulatory issues and governance of PHD; (3) education of all stakeholders about AI technology; and (4) value-based health care including "allocative value," "technology value," and "personalized value."

Dataset Information

Exploring and visualizing multidimensional data in translational research platforms.

Publications

Exploring and visualizing multidimensional data in translational research platforms.

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