These authors contributed equally to this work.
A Skeletal Gene Database
Article first published online: 1 NOV 2000
Copyright © 2000 ASBMR
Journal of Bone and Mineral Research
Volume 15, Issue 11, pages 2095–2122, November 2000
How to Cite
Ho, N. C., Jia, L., Driscoll, C. C., Gutter, E. M., Francomano, C. A. and Drezner, M. K. (2000), A Skeletal Gene Database. J Bone Miner Res, 15: 2095–2122. doi: 10.1359/jbmr.2000.15.11.2095
- Issue published online: 2 DEC 2009
- Article first published online: 1 NOV 2000
- Manuscript Accepted: 15 MAY 2000
- Manuscript Revised: 1 MAY 2000
- Manuscript Received: 15 DEC 1999
- Skeletal Gene Database;
- Skeletal Genome Anatomy Project (SGAP)
Systematic organization of documented data coupled with ready accessibility is of great value to research. Catalogs and databases are created specifically to meet this purpose. The Skeletal Gene Database evolves as part of the Skeletal Genome Anatomy Project (SGAP), an ongoing multi-institute collaborative effort, to study the functional genome of bone and other skeletal tissues. The primary objective of the Skeletal Gene Database is to create a contemporary list of skeletal-related genes, offering the following information for each gene: gene name, protein name, cellular function, disease(s) caused by mutation of the corresponding gene, chromosomal location, LocusLink number, gene size, exon/intron numbers, messenger RNA (mRNA) coding region size, protein size/molecular weight, Online Mendelian Inheritance in Man (OMIM) number of the gene, UniGene assignment, and PubMed reference. The database includes genes already known and published in the literature as well as novel genes not yet characterized but known to be expressed in skeletal tissue. It will be posted on the web for easy access and swift referencing. The data will be updated in tempo with current and future research, thereby providing an invaluable service to the scientific community interested in obtaining information on bone-related genes.
THE SKELETAL Gene Database evolves as part of the Skeletal Genome Anatomy Project (SGAP), begun in 1997 and initiated by the Medical Genetics Branch of the National Human Genome Research Institutes of National Institutes of Health (NIH). The aims of SGAP are (1) to provide a comprehensive resource for scientists interested in both normal and abnormal skeletal growth and development, (2) to catalog a library of genes/expressed sequence tags (ESTs), with particular emphasis on genes/ESTs specifically expressed in skeletal tissues and, (3) to function as a tissue bank, storing normal and abnormal bone, cartilage, tendon, ligament, and synovium.(1)
The Skeletal Gene Database is designed in three phases. The first phase involves cataloguing known skeletal-related genes, the mutations of which are causally associated with human and murine diseases. This catalog summarizes the results of phase I and phase II. The information has been collected and assembled from a variety of online sources, including Online Mendelian Inheritance in Man (OMIM),(2) PubMed,(3) Unigene,(4) LocusLink,(5) Genecard,(6) SwissProt,(7)and the National Center for Biotechnology Information (NCBI) Entrez.(8) The second step concentrates on genes that are already documented in the literature and are known to have a major role in the physiological process of skeletogenesis but are not, at this point of time, known to be associated with diseases. The third stage will focus on newly discovered novel genes expressed in skeletal-related tissues.
This database supplies reference numbers and links to OMIM, Unigene, PubMed, and LocusLink relevant to the gene in question. OMIM, containing over 10,000 entries, offers textual and reference information on human genes and genetic disorders as well as fostering links to the Entrez database of the NCBI, thereby providing access to Medline articles and sequence information. The Unigene system is designed to gather clusters containing sequences of well-characterized genes and novel ESTs representing newly discovered genes. It also gives information on chromosomal localization of a specific gene or EST and its tissue expression. PubMed concentrates on biomedical literature and provides accessibility to literature citations as well as links to full-text journal articles. The PubMed reference for each gene in our catalog is the original description of the gene or a recent review. LocusLink provides information about genetic loci, official nomenclature, aliases, sequence accessions, phenotypes, map information, and related web sites.
To date, there are approximately 1.6 million human ESTs of which 16,400, previously characterized and new, are known to be skeletal-related.(9) This version of the database encompasses phase I and phase II of the Skeletal Gene Database and includes an up-to-date catalog of disease-causing skeletal-related genes.
Please refer to the Skeletal Gene Database located at the end of the article.
Organized documented data coupled with ready accessibility are of great value to research in human development and disease. The rapid advancement of innovative genomic technology together with the explosion of knowledge witnessed in recent decades on gene and protein sequence, structure, organization, position, expression, and function call for establishment of catalogs and databases to afford rapid referencing. Each database presently in existence covers a myriad of topics as well as furnishing links to related databases, facilitating swift and efficient retrieval of information electronically.
The Skeletal Gene Database concentrates on skeletal-related genes that are already known and those that are newly discovered. It is presently undergoing construction and will be available on the web in November 2000. The data provided will be succinct and current and will continue to be updated as new information comes through. This project will contribute toward understanding the functional genome of bone and bone-related tissues and will be a valuable aid and useful search tool to scientists and physicians interested in topics and research on the skeleton.
We thank Dr. Annemarie Sommer for advise and support.
- 11997 SGAP: The skeletal genome anatomy project. Am J Hum Genet 61:A378., , , , , , , , , , , , , , , ,
- 2Online Mendelian Inheritance in Man (OMIM) 1999 OMIM, National Center for Biotechnology Information, National Library of Medicine. http://www.ncbi.nlm.nih.gov/Omim.
- 3National Center for Biotechnology Information (NCBI) 1999 PubMed. NCBI, National Library of Medicine. http://www.ncbi.nlm.gov/PubMed.
- 4National Center for Biotechnology Information (NCBI) 1999 Unigene. NCBI, National Library of Medicine. http://www.ncbi.nlm.gov/Web/Unigene.
- 5National Center for Biotechnology Information (NCBI) 1999 LocusLink. NCMI, National Library of Medicine. http://www.ncbi.nlm.nih.gov/LocusLink.
- 6Weizmann Institute (WI) 1999 Genecard. Weizmann Institute of Genome and Bioinformatics. http://bioinformatics.weizmann.ac.il/cards.
- 7EMBL 1999 Swiss-Prot. Outstation European Bioinformatics Institute. http://www.ebi.ac.uk/Swiss-Prot.
- 8National Center for Biotechnology Information (NCBI) 1998 Entrez. NCBI, National Library of Medicine. http://www.ncbi.nlm.gov/Entrez.
- 9National Center for Biotechnology Information (NCBI) 1999 dbEST. NCBI, National Library of Medicine. http://www.ncbi.nlm.nih.gov/dbEST/dbESTsummaryhtml.