Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework

• Published in: PloS one 2015-04, Vol.10 (3), p.e0122978-e0122978
• Main Authors: Arighi, Cecilia, Shamovsky, Veronica, Masci, Anna Maria, Ruttenberg, Alan, Smith, Barry, Natale, Darren A, Wu, Cathy, D'Eustachio, Peter
• Format: Article
• Language: English
• Subjects: Animals; Annotations; Biochemistry; Bioinformatics; Biological Ontologies; Cellular biology; Chickens; Computational Biology - methods; Controlled vocabularies; Cytokines; Drosophila; Evolution, Molecular; Genomes; Humans; Immune system; Immunology; Information sources; Insects; Ligands; Mice; Molecular Sequence Annotation; Ontology; Poultry; Protein Transport; Proteins; Signal Transduction; Signaling; Species; Structure-function relationships; TLR3 protein; Toll-like receptors; Toll-Like Receptors - metabolism; Vertebrates
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0122978

The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps.