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

## TL;DR

RNAcare is a new platform that helps clinicians analyze gene expression data alongside clinical information, using rheumatoid arthritis as an example to explore how genes relate to symptoms like pain and fatigue.

## Contribution

RNAcare introduces a novel platform that integrates transcriptomic and clinical data for real-time analysis and hypothesis generation in a clinical context.

## Key findings

- RNAcare links inflammation-related genes to pain and fatigue in rheumatoid arthritis patients.
- The platform detects gene expression signatures associated with drug response in RA.
- RNAcare supports user-generated data and published datasets for flexible analysis.

## Abstract

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.

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.

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/.

The online version contains supplementary material available at 10.1186/s12920-025-02162-z.