In addition to annotating alternative isoforms with biological data, APPRIS selects a principal isoform from among the isoforms annotated for each gene. The selection of a principal isoform by APPRIS is based on two principles. The first principle is that there is often one isoform that performs the main cellular function or that is expressed in the majority tissues or in most stages of development, and that the rest of the annotated isoforms are alternatively spliced isoforms that may perform distinct roles. Proteomics evidence suggests that this seems to hold true for many genes (32–37) although there are genes for which it is more difficult to define a principal isoform precisely because there are a number of isoforms that might be regarded as equally important for cellular function.
