Among the functional omics, transcriptomics contributes a global view of gene expression in a cell, tissue or organism, under a given condition and time period. Data derived from RNA sequencing experiments (RNA-seq) allow to unravel how organisms respond to environmental stimuli, as well as study development processes and genes associated to a certain trait, in order to achieve a better understanding of the relations between genes, gene products and gene interactions.
Genetic expression represents the fundamental level at which the genotypes gives place to the phenotype. Essentially, an organism’s cells contain the same genetic information, however, not all genes are active at the same time or are expressed at the same level. This results in different gene expression profiles for a cell depending on a specific condition, environment or moment. Furthermore, gene expression is also related to the unique characteristics of a given cell or tissue type, enabling an organism to be structured in its diverse tissues, organs, and systems, each with distinct gene expression profiles.
Identifying genes that are differentially expressed between contrasting conditions (e.g. different cell or tissue types, environmental conditions, illness or health, developmental stages, among others) is fundamental to understanding one of the molecular basis of phenotypic variation. Thus, expression profile data helps to search for differentially expressed genes that could be associated to cellular responses, which can then be applied as biomarkers or genetic markers for traits of interest.
We refer to coexpression when two genes show associated gene expression profiles, which can indicate related gene function. This knowledge contributes to discovering or predicting new gene function, based on the known function of a gene with associated expression. Accordingly, many genes are coexpressed at a transcript level (mRNA) when their gene products –proteins- interact as protein complexes or in a shared metabolic pathway in the cell. The set of all known interactions between coexpressed genes is called a coexpression network.