All cells in an organism (e.g., cells in a human body) have an identical genome, but they form different cell types ( types in human) for different cellular activities. Obviously not all genes are expressed (turned on) at the same time. How different cell types develop from a fertilized egg during the organism's developmental stages and the entire life is determined by Cell differentiation, which causes different gene expressions in different cells, resulting from the in teraction of the large number of genes in the organism.
Transcription factors and binding sites:
A kind of proteins called transcription factors can attach (bind) to specific parts of the DNA, called binding sites (short combinations of A, T, C or G), located in promoter regions. Specific promoters are associated with particular genes and are generally close to the respective genes. (There are over 200 known transcription factors in yeast, over 600 in worm and fly, and over 1500 in weeds.)
Gene regulation networks:
These interactions can be described as gene regulation networks (gene circuits). Understanding, describing and modeling such gene regulation networks are one of the most challenging problems in functional genomics. Reverse engineering is required to reconstruct the gene networks from the observed gene expression data (e.g., expression levels as functions of time).