A framework for comparing phenotype annotations of orthologous genes.
OBJECTIVE
Animal models are a key resource for the investigation of human diseases. In contrast to functional annotation, phenotype annotation is less standard, and comparing phenotypes across species remains challenging. The objective of this paper is to propose a framework for comparing phenotype annotations of orthologous genes based on the Medical Subject Headings (MeSH) indexing of biomedical articles in which these genes are discussed.


METHODS
17,769 pairs of orthologous genes (mouse and human) are downloaded from the Mouse Genome Informatics (MGI) system and linked to biomedical articles through Entrez Gene. MeSH index terms corresponding to diseases are extracted from Medline.


RESULTS
11,111 pairs of genes exhibited at least one phenotype annotation for each gene in the pair. Among these, 81% have at least one phenotype annotation in common, 80% have at least one annotation specific to the human gene and 84% have at least one annotation specific to the mouse gene. Four disease categories represent 54% of all phenotype annotations.


CONCLUSIONS
This framework supports the curation of phenotype annotation and the generation of research hypotheses based on comparative studies.
Bodenreider
Olivier
O
US National Library of Medicine, NIH, Bethesda, USA. olivier@nlm.nih.gov
Burgun
Anita
A
D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D005796:Genes; D006801:Humans; D016239:MEDLINE; D046650:Medical Subject Headings; D051379:Mice; D010641:Phenotype; D014481:United States