INTERFEROME: the database of interferon-regulated genes

Full description

THE DATABASE OF INTERFERON-REGULATED GENES

This database is an upgrade of the original Interferome database and contains type I, II and III interferon-regulated genes, manually curated from publicly available microarray datasets.

INTRODUCTION

Interferons (IFNs) were identified as antiviral proteins more than 50 years ago and since then have been shown to regulate cell proliferation, survival, migration and specialised functions. Consequently they are involved in numerous homeostatic and pathological processes including infections, cancer, autoimmunity, inflammation and metabolic disorders. These cytokines are also used as therapeutics in diseases such as chronic viral infections, cancer and multiple sclerosis. IFNs potentially regulate the transcription of up to 2000 genes in an IFN subtype, dose, cell type and stimulus dependent manner. This database of IFN-regulated genes is an attempt at integrating information from high-throughput experiments to gain a detailed understanding of the various IFN-activated pathways that regulate subsets of genes to enhance our understanding of pathophysiological processes.

DEFINITIONS

IFN-regulated genes (IRGs) were identified from experiments where cells or organisms were treated with an IFN. Genes that were significantly up- or down-regulated relative to control samples were defined as IRGs, annotated and uploaded into the database. We have set a default limit of 2-fold change in expression for searches because this is a commonly accepted parameter; although the option remains to change this when implementing a search.

DATABASE SCOPE

This database will enable the reliable identification of an individual IRG or IRG signatures from high-throughput data sets (i.e., microarray, RNA-seq, proteomic data, etc.). It will also assist in identifying regulatory elements, chromosomal location and tissue expression of IRGs in human and mouse. This upgraded version, Interferome v2.0, has quantitative data, more detailed annotation and search capabilities and can be queried for one gene or thousands, as in a gene list from am RNA-seq experiment.