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. 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. 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.
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 . 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 . 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 .
Which is the most common gene signature in Rheumatoid Arthritis patients?
Which is the most common gene signature in Rheumatoid Arthritis patients ?
IFN signature
Interferon signature IFN signature