You are here

Proc Natl Acad Sci U S A DOI:10.1073/pnas.0709013104

Distinguishing protein-coding and noncoding genes in the human genome.

Publication TypeJournal Article
Year of Publication2007
AuthorsClamp, M, Fry, B, Kamal, M, Xie, X, Cuff, J, Lin, MF, Kellis, M, Lindblad-Toh, K, Lander, ES
JournalProc Natl Acad Sci U S A
Date Published2007 Dec 04
KeywordsAnimals, Base Sequence, DNA Transposable Elements, Dogs, Genes, Genetic Code, Genome, Human, Genomics, Humans, Mice, Molecular Sequence Data, Open Reading Frames, Proteins, Pseudogenes, Sequence Analysis, DNA

Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of approximately 24,500 putative protein-coding genes. It is broadly suspected that a large fraction of these entries are functionally meaningless ORFs present by chance in RNA transcripts, because they show no evidence of evolutionary conservation with mouse or dog. However, there is currently no scientific justification for excluding ORFs simply because they fail to show evolutionary conservation: the alternative hypothesis is that most of these ORFs are actually valid human genes that reflect gene innovation in the primate lineage or gene loss in the other lineages. Here, we reject this hypothesis by carefully analyzing the nonconserved ORFs-specifically, their properties in other primates. We show that the vast majority of these ORFs are random occurrences. The analysis yields, as a by-product, a major revision of the current human catalogs, cutting the number of protein-coding genes to approximately 20,500. Specifically, it suggests that nonconserved ORFs should be added to the human gene catalog only if there is clear evidence of an encoded protein. It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes.


Alternate JournalProc. Natl. Acad. Sci. U.S.A.
PubMed ID18040051
PubMed Central IDPMC2148306
Grant ListR01 HG004037 / HG / NHGRI NIH HHS / United States
R01 HG004037-01A1 / HG / NHGRI NIH HHS / United States