Visualizing omics and clinical data: Which challenges for dealing with their variety?

ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities

MOTIVATION

High-throughput technologies yield a broad spectrum of multi-omics datasets, which offer unparalleled insights into complex biological systems. However, effectively analyzing this diverse array of data presents challenges, considering factors such as species diversity, data types, costs, and limitations of the available tools.

RESULTS

Herein, we present ExpOmics, a comprehensive web platform featuring 7 applications and 4 toolkits, with 28 customizable analysis functions spanning various analyses of differential expression, co-expression, Weighted Gene Co-expression Network Analysis (WGCNA), feature selection, and functional enrichment. ExpOmics allows users to upload and explore multi-omics data without organism restrictions, supporting various expression data, including genes, mRNAs, lncRNAs, miRNAs, circRNAs, piRNAs, and proteins and is compatible with diverse gene nomenclatures and expression values. Moreover, ExpOmics enables users to analyze 22 427 transcriptomic datasets of 196 cancer subtypes sourced from 63 projects of The Cancer Genome Atlas Program (TCGA) to identify cancer biomarkers. The analysis results from ExpOmics are presented in high-quality graphical formats suitable for publication and are available for free download. A case study using ExpOmics identified two potential oncogenes, SERPINE1 and SLC43A1, that may regulate colorectal cancer through distinct biological processes. In summary, ExpOmics can serves as a robust platform for global researchers to explore multi-omics data, gain biological insights, and formulate testable hypotheses.

AVAILABILITY AND IMPLEMENTATION

ExpOmics is available at http://www.biomedical-web.com/expomics.

Precision public health, the key for future outbreak management: A scoping review

Background

Precision Public Health (PPH) is a newly emerging field in public health medicine. The application of various types of data allows PPH to deliver more tailored interventions to a specific population within a specific timeframe. However, the application of PPH possesses several challenges and limitations that need to be addressed.

Objective

We aim to provide evidence of the various use of PPH in outbreak management, the types of data that could be used in PPH application, and the limitations and barriers in the application of the PPH approach.

Methods and analysis

Articles were searched in PubMed, Web of Science, and Science Direct. Our selection of articles was based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) for Scoping Review guidelines. The outcome of the evidence assessment was presented in narrative format instead of quantitative.

Results

A total of 27 articles were included in the scoping review. Most of the articles (74.1%) focused on PPH applications in performing disease surveillance and signal detection. Furthermore, the data type mostly used in the studies was surveillance (51.9%), environment (44.4), and Internet query data. Most of the articles emphasized data quality and availability (81.5%) as the main barriers in PPH applications followed by data integration and interoperability (29.6%).

Conclusions

PPH applications in outbreak management utilize a wide range of data sources and analytical techniques to enhance disease surveillance, investigation, modeling, and prediction. By leveraging these tools and approaches, PPH contributes to more effective and efficient outbreak management, ultimately reducing the burden of infectious diseases on populations. The limitation and challenges in the application of PPH approaches in outbreak management emphasize the need to strengthen the surveillance systems, promote data sharing and collaboration among relevant stakeholders, and standardize data collection methods while upholding privacy and ethical principles.

ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data

In the era of life-omics, huge amounts of multi-omics data have been generated and widely used in biomedical research. It is challenging for biologists with limited programming skills to obtain biological insights from multi-omics data. Thus, a biologist-oriented platform containing visualization functions is needed to make complex omics data digestible. Here, we propose an easy-to-use, interactive web server named ExpressVis. In ExpressVis, users can prepare datasets; perform differential expression analysis, clustering analysis, and survival analysis; and integrate expression data with protein–protein interaction networks and pathway maps. These analyses are organized into six modules. Users can use each module independently or use several modules interactively. ExpressVis displays analysis results in interactive figures and tables, and provides comprehensive interactive operations in each figure and table, between figures or tables in each module, and among different modules. It is freely accessible at https://omicsmining.ncpsb.org.cn/ExpressVis and does not require login. To test the performance of ExpressVis for multi-omics studies of clinical cohorts, we re-analyzed a published hepatocellular carcinoma dataset and reproduced their main findings, suggesting that ExpressVis is convenient enough to analyze multi-omics data. Based on its complete analysis processes and unique interactive operations, ExpressVis provides an easy-to-use solution for exploring multi-omics data.

Convergence of Precision Medicine and Public Health Into Precision Public Health: Toward a Big Data Perspective

The field of precision medicine explores disease treatments by looking at genetic, socio-environmental, and clinical factors, thus trying to provide a holistic view of a person's health. Public health, on the other hand, is focused on improving the health of populations through preventive strategies and timely interventions. With recent advances in technology, we are able to collect, analyze and store for the first-time large volumes of real-time, diverse and continuous health data. Typically, the field of precision medicine deals with a huge amount of data from few individuals; public health, on the other hand, deals with limited data from a population. With the coming of Big Data, the fields of precision medicine and public health are converging into precision public health, the study of biological and genetic factors supported by large amounts of population data. In this paper, we explore through a comprehensive review the data types and use cases found in precision medicine and public health. We also discuss how these data types and use cases can converge toward precision public health, as well as challenges and opportunities provided by research and analyses of health data.

Interpretation of omics data analyses

Omics studies attempt to extract meaningful messages from large-scale and high-dimensional data sets by treating the data sets as a whole. The concept of treating data sets as a whole is important in every step of the data-handling procedures: the pre-processing step of data records, the step of statistical analyses and machine learning, translation of the outputs into human natural perceptions, and acceptance of the messages with uncertainty. In the pre-processing, the method by which to control the data quality and batch effects are discussed. For the main analyses, the approaches are divided into two types and their basic concepts are discussed. The first type is the evaluation of many items individually, followed by interpretation of individual items in the context of multiple testing and combination. The second type is the extraction of fewer important aspects from the whole data records. The outputs of the main analyses are translated into natural languages with techniques, such as annotation and ontology. The other technique for making the outputs perceptible is visualization. At the end of this review, one of the most important issues in the interpretation of omics data analyses is discussed. Omics studies have a large amount of information in their data sets, and every approach reveals only a very restricted aspect of the whole data sets. The understandable messages from these studies have unavoidable uncertainty.

Metabolic Network Reconstructions to Predict Drug Targets and Off-Target Effects

The drug development pipeline has stalled because of the difficulty in identifying new drug targets while minimizing off-target effects. Computational methods, such as the use of metabolic network reconstructions, may provide a cost-effective platform to test new hypotheses for drug targets and prevent off-target effects. Here, we summarize available methods to identify drug targets and off-target effects using either reaction-centric, gene-centric, or metabolite-centric approaches with genome-scale metabolic network reconstructions.

Using R and Bioconductor in Clinical Genomics and Transcriptomics

Bioinformatics pipelines are essential in the analysis of genomic and transcriptomic data generated by next-generation sequencing (NGS). Recent guidelines emphasize the need for rigorous validation and assessment of robustness, reproducibility, and quality of NGS analytic pipelines intended for clinical use. Software tools written in the R statistical language and, in particular, the set of tools available in the Bioconductor repository are widely used in research bioinformatics; and these frameworks offer several advantages for use in clinical bioinformatics, including the breath of available tools, modular nature of software packages, ease of installation, enforcement of interoperability, version control, and short learning curve. This review provides an introduction to R and Bioconductor software, its advantages and limitations for clinical bioinformatics, and illustrative examples of tools that can be used in various steps of NGS analysis.