Abstract
BackgroundDiseases of cartilage, such as arthritis and degenerative disc disease, affect the majority of the general population, particularly with ageing. Discovery and understanding of the genes and pathways involved in cartilage biology will greatly assist research on the development, degeneration and disorders of cartilage.DescriptionWe have established the Integrated Cartilage Gene Database (iCartiGD) of genes that are known, based on results from high throughput experiments, to be expressed in cartilage. Information about these genes is extracted automatically from public databases and presented as a single page report via a web-browser. A variety of flexible search options are provided and the chromosomal distribution of cartilage associated genes can be presented.ConclusioniCartiGD provides a comprehensive source of information on genes known to be expressed in cartilage. It will remain current due to its automatic update capability and provide researchers with an easily accessible resource for studies involving cartilage. Genetic studies of the development and disorders of cartilage will benefit from this database.
Highlights
Diseases of cartilage, such as arthritis and degenerative disc disease, affect the majority of the general population, with ageing
An ever expanding amount of information that would be of interest to biologists and clinicians who study cartilage is being gathered in a wide range of databases
If these data are to be utilised effectively, coordination of the resources should prove an invaluable help to the research community. iCartiGD has been developed to provide a single point of entry for cartilage biologists into this wealth of knowledge
Summary
Diseases of cartilage, such as arthritis and degenerative disc disease, affect the majority of the general population, with ageing. SAGE libraries derived from chondrosarcomas, and microarray studies and a cDNA library of normal cartilage complete the cartilage tissue data set This gives a total of approximately 14,000 genes (based on EntrezGene identifiers) that are expressed in at least one cartilage tissue type. NCBI Entrez Gene UniGene MapViewer HomoloGene dbEST SAGEmap PubMed OMIM GEO RefSeq dbSNP Ensembl UniProt PDB Sage Genie InterPro HapMap Affymetrix SymAtlas UCSC genome browser GOA KEGG http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene http://www.ncbi.nlm.nih.gov/mapview http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene http://www.ncbi.nlm.nih.gov/dbEST/index.html http://www.ncbi.nlm.nih.gov/SAGE/ http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM http://www.ncbi.nlm.nih.gov/geo/ http://www.ncbi.nlm.nih.gov/RefSeq/ http://www.ncbi.nlm.nih.gov/SNP/index.html http://www.ensembl.org http://www.uniprot.org http://www.rcsb.org/pdb http://cgap.nci.nih.gov/SAGE http://www.ebi.ac.uk/interpro http://www.hapmap.org http://www.affymetrix.com http://wombat.gnf.org/SymAtlas http://genome.ucsc.edu http://www.ebi.ac.uk/GOA http://www.genome.jp/kegg/kegg2.html This allows iCartiGD to take account of frequent modifications to databases such as UniGene and to provide the correct mappings from UniGene to the latest version of EntrezGene. Rebuilding the database from the current versions of the source databases ensures all modifications to the data are obtained
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