Journal Article

RNAcare: integrating clinical data with transcriptomic evidence using rheumatoid arthritis as a case study

Goodyear, Carl, Porter, Duncan, Tang, Mingcan, Morton, Fraser, Otto, Thomas D., Siebert, Stefan, Haese-Hill, William

2025

Overview

Background Gene expression analysis is a crucial tool for uncovering the biological mechanisms that underlie differences between patient subgroups, offering insights that can inform clinical decisions. However, despite its potential, gene expression analysis remains challenging for clinicians due to the specialised skills required to access, integrate, and analyse large datasets. Existing tools primarily focus on RNA-Seq data analysis, providing user-friendly interfaces but often falling short in several critical areas: they typically do not integrate clinical data, lack support for patient-specific analyses, and offer limited flexibility in exploring relationships between gene expression and clinical outcomes in disease cohorts. Users, including clinicians with a general knowledge of transcriptomics, however, who may have limited programming experience, are increasingly seeking tools that go beyond traditional analysis. To overcome these issues, computational tools must incorporate advanced techniques, such as machine learning, to better understand how gene expression correlates with patient symptoms of interest. Results Our RNAcare platform, addresses these limitations by offering an interactive and reproducible solution specifically designed for analysing transcriptomic data from patient samples in a clinical context. This enables researchers to directly integrate gene expression data with clinical features, perform exploratory data analysis, and identify patterns among patients with similar diseases. By enabling users to integrate transcriptomic and clinical data, and customise the target label, the platform facilitates the analysis of the relationships between gene expression and clinical symptoms like pain and fatigue. This allows users to generate hypotheses and illustrative visualisations/reports to support their research. As proof of concept, we use RNAcare to link inflammation-related genes to pain and fatigue in rheumatoid arthritis (RA) and detect signatures in the drug response group, confirming previous findings. Conclusion We present a novel computational platform allowing the interpretation of clinical and transcriptomics data in real-time. The platform can be used for data generated by the user, such as the patient data presented here or using published datasets. The platform is available at https://rna-care.mvls.gla.ac.uk/ , and its source code is https://github.com/sii-scRNA-Seq/RNAcare/ .

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Arthritis / Arthritis, Rheumatoid - genetics / Arthritis, Rheumatoid - pathology / Biomedical and Life Sciences / Biomedicine / Case studies / Chronic illnesses / Computational Biology - methods / Computer applications / Data visualisation / Datasets / Diagnosis / Fatigue / Gene Expression / Gene expression analysis / Gene Expression Profiling / Genes / Genetic aspects / Human Genetics / Humans / Inflammation / Information management / Machine learning / Methods / Microarrays / Pain / Patient clinic data / Patients / Rheumatic diseases / Rheumatoid arthritis / Rheumatoid factor / Risk factors / RNA / RNA sequencing / Software / Transcriptome / Transcriptomics / Web applications / Webserver