Bioinformatics Genetics

Differential Expression of Genes

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Gene expression is the process in which information from a gene is used in the synthesis of a functional gene product called protein but in non-protein-coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA. Gene expression is summarized in the Central Dogma first proposed by Francis Crick in 1958, after that developed in his 1970 article, and expanded by the subsequent discoveries of reverse transcription and RNA replication. 

The process of gene expression happens in all types of cells including multicellular organisms such as eukaryotes and bacteria and archaea such as prokaryotes and used by viruses to produce the macromolecular machinery for life.

In genetics, gene expression is the most basic and important level at which the genotype gives rise to the phenotype, such as an observable trait. The genetic information stored in DNA shows the genotype, whereas the phenotype results from the “interpretation” of that information. Such phenotypes are often expressed by the synthesis of proteins that control the organism’s structure and development, or that act as enzymes catalyzing specific metabolic pathways.

All the steps in the gene expression process are;

  • Regulation
  • The transcription
  • RNA splicing
  • Translation 
  • Post-translational modification of a protein

Regulation of gene expression is the basis for cellular differentiation, development, morphogenesis and the versatility and adaptability of any organism. Gene regulation may therefore serve as a substrate for evolutionary change.

The reason behind studying the differential gene expression is the rising of the question that if the genome is the same in all somatic cells within an organism, how do the cells become different from one another? If every cell in the body has the genes for hemoglobin and insulin proteins, how are the hemoglobin proteins made only in the red blood cells, the insulin proteins made only in certain pancreas cells, and neither made in the kidney or nervous system? On the basis of the embryological evidence for genomic equivalence and on bacterial models of gene regulation, a consensus appeared in the 1960s that cells differentiate through differential gene expression. The three main postulates given are as follows:

  1. Every cell nucleus has the complete genome made in the fertilized egg. In molecular terms, the DNAs of all differentiated cells are identical.
  2. The unused genes in differentiated cells are not destroyed or mutated, and they retain the potential for being expressed.
  1. Only a small percentage of the genome is expressed in each cell, and a portion of the synthesized RNA in the cell is specific for that cell type.

Differential gene expression analysis

Differential expression analysis means taking the normalized read count data and performing statistical analysis to find out quantitative changes in expression levels between experimental groups of organisms. 


Different methods for differential expression analysis are edgeR and DESeq that are on the basis of negative binomial (NB) distributions or baySeq and EBSeq which are Bayesian techniques and approaches on the basis of negative binomial models. Tools used for the   differential expression can perform pairwise comparison, others such as edgeR, limma-voom, DESeq and maSigPro can perform multiple comparisons.

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