Gene signature
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A gene signature or gene expression signature is a single or combined group of genes in a cell with a uniquely characteristic pattern of gene expression[1] that occurs as a result of an altered or unaltered biological process or pathogenic medical condition.[2] This is not to be confused with the concept of gene expression profiling. Activating pathways in a regular physiological process or a physiological response to a stimulus results in a cascade of signal transduction and interactions that elicit altered levels of gene expression, which is classified as the gene signature of that physiological process or response.[3] The clinical applications of gene signatures breakdown into prognostic, diagnostic[4][5] and predictive signatures. The phenotypes that may theoretically be defined by a gene expression signature range from those that predict the survival or prognosis of an individual with a disease, those that are used to differentiate between different subtypes of a disease, to those that predict activation of a particular pathway. Ideally, gene signatures can be used to select a group of patients[6] for whom a particular treatment will be effective.[7][8]
In 1995, 2 studies conducted identified unique approaches to analyzing global gene expression of a genome which collectively promoted the value of identifying and analyzing gene signatures for physiological relevance. The first study reports a technique that improves expressed sequence tag (EST) analysis, known as Serial Analysis of Gene Expression (SAGE) that hinged on sequencing and quantifying mRNA samples which acquired levels of gene expression that eventually revealed characteristic gene expression patterns.[9]
The second study identified a technique that is now widely known as the microarray which quantifies complementary DNA (cDNA) hybridization on a glass slide to analyze the expression of many genes in parallel.[10] These studies drew greater attention to the wealth of information that analysis of gene signatures bear that may or may not be physiologically relevant.
Pressing forward, the latter technique has revolutionized research in genetics and DNA chip technology[11] as it is a widely adopted technique to profile gene expression signatures such that these physiological responses can be cataloged[12] in repositories such as NCBI Gene Expression Omnibus. This catalogue of prognostic, diagnostic and predictive gene expression signatures allow for predictions of onset of pathogenic diseases in patients,[13] tumour and cancer classification,[14] and enhanced therapeutic strategies that predict the optimal target candidates subjects and genes.[15]
Today, microarrays and other quantitative methods such as RNA-seq that encompass gene expression profiling, are moving towards promotion of re-analysis and integration of the large, publicly available database of gene expression signatures and profiles to uncover the full threshold of information these expression signatures hold.[16]