Importance of Correlation between Gene Expression Levels: Application to the Type I Interferon Signature in Rheumatoid Arthritis

Frédéric Reynier, Fabien Petit, Malick Paye, Fanny Turrel-Davin, Pierre-Emmanuel Imbert, Arnaud Hot, Bruno Mougin and Pierre Miossec

PLOS ONE, 2011, vol. 6, issue 10, 1-8

Abstract: Background: The analysis of gene expression data shows that many genes display similarity in their expression profiles suggesting some co-regulation. Here, we investigated the co-expression patterns in gene expression data and proposed a correlation-based research method to stratify individuals. Methodology/Principal Findings: Using blood from rheumatoid arthritis (RA) patients, we investigated the gene expression profiles from whole blood using Affymetrix microarray technology. Co-expressed genes were analyzed by a biclustering method, followed by gene ontology analysis of the relevant biclusters. Taking the type I interferon (IFN) pathway as an example, a classification algorithm was developed from the 102 RA patients and extended to 10 systemic lupus erythematosus (SLE) patients and 100 healthy volunteers to further characterize individuals. We developed a correlation-based algorithm referred to as Classification Algorithm Based on a Biological Signature (CABS), an alternative to other approaches focused specifically on the expression levels. This algorithm applied to the expression of 35 IFN-related genes showed that the IFN signature presented a heterogeneous expression between RA, SLE and healthy controls which could reflect the level of global IFN signature activation. Moreover, the monitoring of the IFN-related genes during the anti-TNF treatment identified changes in type I IFN gene activity induced in RA patients. Conclusions: In conclusion, we have proposed an original method to analyze genes sharing an expression pattern and a biological function showing that the activation levels of a biological signature could be characterized by its overall state of correlation.

Date: 2011
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0024828

DOI: 10.1371/journal.pone.0024828

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