OKCAM: An ontology-based, human-centered knowledgebase for cell adhesion molecules

Chuan Yun Li, Qing Rong Liu, Pingwu Zhang, Xiao Mo Li, Liping Wei, George R. Uhl

Research output: Contribution to journalArticle

Abstract

'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.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume37
Issue numberSUPPL. 1
DOIs
StatePublished - 2009
Externally publishedYes

Fingerprint

Knowledge Bases
Cell Adhesion Molecules
Genes
Molecular Sequence Annotation
Gene Ontology
Information Systems
Cell Adhesion
Cell Communication
Nervous System
Psychiatry
Phenotype
Brain

ASJC Scopus subject areas

  • Genetics

Cite this

OKCAM : An ontology-based, human-centered knowledgebase for cell adhesion molecules. / Li, Chuan Yun; Liu, Qing Rong; Zhang, Pingwu; Li, Xiao Mo; Wei, Liping; Uhl, George R.

In: Nucleic Acids Research, Vol. 37, No. SUPPL. 1, 2009.

Research output: Contribution to journalArticle

Li, Chuan Yun ; Liu, Qing Rong ; Zhang, Pingwu ; Li, Xiao Mo ; Wei, Liping ; Uhl, George R. / OKCAM : An ontology-based, human-centered knowledgebase for cell adhesion molecules. In: Nucleic Acids Research. 2009 ; Vol. 37, No. SUPPL. 1.
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