OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules.
'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.
Li
Chuan-Yun
CY
Molecular Neurobiology Branch, NIH-IRP (NIDA), Baltimore, MD 21224, USA.
Liu
Qing-Rong
QR
Zhang
Ping-Wu
PW
Li
Xiao-Mo
XM
Wei
Liping
L
Uhl
George R
GR
D000818:Animals; D015815:Cell Adhesion Molecules / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D030562:Databases, Protein; D006801:Humans; D051379:Mice; D051381:Rats; D014584:User-Computer Interface
D015815:Cell Adhesion Molecules
Bull Med Libr Assoc. 2000 Jul;88(3):265-6
10928714
Nature. 2007 Jan 11;445(7124):168-76
17151600
Am J Hum Genet. 2008 Jan;82(1):160-4
18179894
Nucleic Acids Res. 2003 Jan 1;31(1):248-50
12519993
Nat Genet. 2000 May;25(1):25-9
10802651
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W169-75
17576678
Nucleic Acids Res. 2008 Jan;36(Database issue):D773-9
18086701
Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):1100-5
9927700
Nat Genet. 2005 May;37(5):495-500
15806104
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D622-7
16381945
Arch Gen Psychiatry. 2008 Jun;65(6):683-93
18519826
Mamm Genome. 2007 Sep;18(9):627-34
17846832
Nucleic Acids Res. 2006 Jul 18;34(12):3465-75
16849434
Curr Opin Neurobiol. 2005 Feb;15(1):73-80
15721747
Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21
18045790
Hum Mol Genet. 2006 May 15;15(10):1659-66
16600991
Am J Med Genet B Neuropsychiatr Genet. 2006 Dec 5;141B(8):918-25
17099884
Annu Rev Neurosci. 2007;30:451-74
17600523
RNA. 2006 Feb;12(2):192-7
16373484
Am J Epidemiol. 2006 Jul 1;164(1):1-4
16641305
Nucleic Acids Res. 2007 Jan;35(Database issue):D156-61
17082204
Methods Mol Biol. 2007;396:59-70
18025686
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W720-4
16845106
Am J Hum Genet. 2008 Jan;82(1):199-207
18179900
Annu Rev Biochem. 2007;76:267-94
17506641
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D115-8
16381827
Front Biosci. 2003 Jan 01;8:d306-55
12456358
Mol Psychiatry. 2005 Apr;10(4):384-92
15452586
Nucleic Acids Res. 1996 Jan 1;24(1):238-41
8594589
Nature. 2007 Oct 18;449(7164):851-61
17943122
Hum Mol Genet. 2007 Dec 1;16(23):2880-91
17804423
Nature. 2004 Jul 1;430(6995):88-93
15190252
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D659-63
16381953
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D411-4
16381900
Bioinformatics. 2005 Oct 1;21(19):3787-93
15817693
Schizophr Bull. 2008 Jan;34(1):9-12
18032396
Nat Genet. 2004 Sep;36(9):949-51
15286789
Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
18077471
FEBS J. 2005 Oct;272(20):5129-48
16218947
Am J Med Genet B Neuropsychiatr Genet. 2006 Dec 5;141B(8):844-53
16894614
Neuron. 2000 Apr;26(1):207-17
10798405
J Endocrinol. 2005 Apr;185(1):19-33
15817824
Nature. 2008 Feb 21;451(7181):998-1003
18288195
Trends Cell Biol. 2005 Apr;15(4):216-21
15817378
Genome Biol. 2005;6(5):R46
15892874
Nucleic Acids Res. 2008 Jan;36(Database issue):D170-2
18000000
Nature. 2006 Nov 23;444(7118):444-54
17122850
Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40
18000002