Nucleic Acids Research Advance Access published online on September 12, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn568
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OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules
1Molecular Neurobiology Branch, NIH-IRP (NIDA), Baltimore, MD 21224, USA and 2Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
To whom correspondence should be addressed. Tel: +1 410 550 2843 x146; Fax: +1 410 550 1535; Email: guhl{at}intra.nida.nih.gov
Received June 24, 2008. Revised August 18, 2008. Accepted August 21, 2008.
‘Cell adhesion molecules’ (CAMs) are essential elements of cell/cell communication that are important for proper development and plasticity of a variety of organs and tissues. In the brain, appropriate assembly and tuning of neuronal connections is likely to require appropriate function of many cell adhesion processes. Genetic studies have linked and/or associated CAM variants with psychiatric, neurologic, neoplastic, immunologic and developmental phenotypes. However, despite increasing recognition of their functional and pathological significance, no systematic study has enumerated CAMs or documented their global features. We now report compilation of 496 human CAM genes in six gene families based on manual curation of protein domain structures, Gene Ontology annotations, and 1487 NCBI Entrez annotations. We map these genes onto a cell adhesion molecule ontology that contains 850 terms, up to seven levels of depth and provides a hierarchical description of these molecules and their functions. We develop OKCAM, a CAM knowledgebase that provides ready access to these data and ontologic system at http://okcam.cbi.pku.edu.cn. We identify global CAM properties that include: (i) functional enrichment, (ii) over-represented regulation modes and expression patterns and (iii) relationships to human Mendelian and complex diseases, and discuss the strengths and limitations of these data.