Volcano Plot View

Interactive 3D volcano plot links to gene expression by pathotype in synovium or blood

Gene View

Compare gene expression levels in synovium or blood with clinical, histological or radiographic markers

Table View

Searchable table of genes upregulated in different groups in synovium

Cell-specific module View

Clinico-radiographic correlates of cell-specific gene modules in synovium

Module View

Modular analysis and module heatmap in synovium or blood compared to pathotype

Module Tables

Searchable tables of module correlations with clinical, histological or radiographic variables

Module Tissue Comparison

Comparison of how well synovium vs blood gene modules correlate with phenotypic variables

PEAC RNA-seq Data

This webpage hosts an interactive resource for the paper 'Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes.', and provides access to RNA-sequencing data from the Pathobiology of Early Arthritis Cohort (PEAC) study.

Key PEAC Publications

• Myles J. Lewis, Michael R. Barnes, Kevin Blighe, Katriona Goldmann, Christopher R. John, Sharmila Rana, Jason Hackney, Nandhini Ramamoorthi, David Watson, Sarah Kummerfeld, Rebecca Hands, Sudeh Riahi, Vidalba Rocher-Ros, Felice Rivellese, Frances Humby, Stephen Kelly, Michele Bombardieri, Nora Ng, Maria DiCicco, Désirée van der Heijde, Robert Landewé, Annette van der Helm-van Mil, Alberto Cauli, Iain B. McInnes, Christopher D. Buckley, Ernest Choy, Peter Taylor, Michael J. Townsend, Costantino Pitzalis "Molecular portraits of early rheumatoid arthritis identify clinical and treatment response phenotypes." Cell reports 28.9 (2019): 2455-2470.. DOI: 10.1016/j.celrep.2019.07.091 PMID: 31461658
• Frances Humby, Myles Lewis, Nandhini Ramamoorthi, Jason A Hackney, Michael R Barnes, Michele Bombardieri, A. Francesca Setiadi, Stephen Kelly, Fabiola Bene, Maria DiCicco, Sudeh Riahi, Vidalba Rocher, Nora Ng, Ilias Lazarou, Rebecca Hands, Désirée van der Heijde, Robert B M Landewé, Annette van der Helm-van Mil, Alberto Cauli, Iain McInnes, Christopher Dominic Buckley, Ernest H Choy, Peter C Taylor, Michael J Townsend, Costantino Pitzalis. "Synovial cellular and molecular signatures in early rheumatoid arthritis stratify clinical response to csDMARD therapy and predict radiographic progression." Ann Rheum Dis 2019; 78(6): 761-772. PMID: 30878974.

Associated Software

Katriona Goldmann and Myles Lewis (2021). volcano3D: Interactive Plotting of Three-Way Differential Expression Analysis. R package version 1.2.0. https://CRAN.R-project.org/package=volcano3D.

Shiny Website

The shiny website was implemented by Myles Lewis, Katriona Goldmann and Vladan Petrovic.