Functional genomics focuses on analyzing the expression of numerous genes. One branch of this field is transcriptomics, which examines transcriptomes—all the RNA transcripts produced by an organism at a specific time. A common approach in transcriptomics involves the creation of DNA microarrays or microchips containing thousands of cDNAs or oligonucleotides. These arrays are hybridized with labeled RNAs (or their corresponding cDNAs) from cells, and the hybridization intensity at each spot indicates the expression level of the corresponding gene. This method enables the simultaneous analysis of the timing and location of expression for multiple genes.

Serial Analysis of Gene Expression (SAGE) identifies which genes are expressed in a particular tissue and measures their expression levels. It works by generating short gene-specific tags from cDNAs, ligating them between linkers, and sequencing the ligated tags to determine gene expression and abundance. Cap Analysis of Gene Expression (CAGE) provides similar data but focuses on the 5'-ends of mRNAs, enabling the identification of transcription start sites and aiding in the localization of promoters.

High-density transcriptional mapping of entire chromosomes has revealed that most sequences in cytoplasmic polyadenylated RNAs originate from non-exon regions of ten human chromosomes. Additionally, nearly half of the transcription from these chromosomes is nonpolyadenylated. These findings suggest that the majority of stable nuclear and cytoplasmic transcripts derive from regions outside exons, which may explain significant differences between species, such as humans and chimpanzees, whose exons are nearly identical.