GDB, what's in it for me? 1996 has brought with it a new release of the human Genome Data Base (GDB)k While maps and mapping related data (i.e. clones, probes and other reagents) remain the primary locus of GDB activ- ities, the database has also greatly ex- panded its ability to capture other bio- logical information. This providt.~ a means for managing functional information about gene families, genes and their prod- ucts. This kind of information is vital for achieving an ultimate goal of human genome research, the understanding of human genetic disease.

Once a gene has been cloned, sequenced and mapped, its normal cel- lular role, and how mutation can result in abnormal function and disease, can be determined. Logical steps in the charac- terization of a newly cloned gene can include comparison against known gene sequences, resulting in the identification of conserved structural and functional protein motifs and. ultimately, the classi- fication of genes into families. Newly cloned genes placed into families are assigned potential functions based on the functions known for already charac- terized members of tile family.

The entry for the P/L¥ gene family exemplifies the goals of the GDB for the representation of biological data

G E N E T W O R K

regarding gene families. While the entry for this gene family was created by the GDB staff, the majority of gene families will be entered by knowledgeable mem- bers of the community, whose research makes them expert in the characteriz- ation of certain gene families. Any mem- ber of the biological research community can enter a gene family into the GDB, maintaining and expanding their entry as necessary.

Data stored in the GDB related to gen¢ families falls into the following cat- cgories: name, aliases, definition, genes, annotations, external links and citations. Aliases are an important concept in the GDB 6.0. representing other names by which an object is commonly known. An alias for the PAX" gene family is 'paired box', which is the name of the protein motif commoa to all members of this family. Genes are also known by several different names, and so aliases are again used to capture all of these possibilities. For example, an alias for the gene PAX6 is "aniridia/keratitis', which demribes a phenotype that was mapped to mu- tations in the P.,L¥6gene.

.Ks the GDB is now a user-editable database, any member of the biological research community can enter aliases for genes, gene families and other database objects. This ultimately results in greater ease in finding the appropriate entry in the database, because users can search on the name that is known to them for genes and gene families.

A definition is provided to describe tile reasons why genes have been grouped into a family. These can include a consensus sequence, such as the 'paired box' domain that is common to all members of the PAX family. Potential functions of genes can also Ix~ included here, such as the proposed role of some PAX" genes as transcription factors. If members of a family also belong to another family or subfamily this can also be noted here, such as the mention that some PAX genes contain a homeolx)x and are, thus. members of the homeobox family.

Currently, the PAY family lists nine human PAX genes, which are hyper- linked to the individual entries that con- tain further information about each gene. Members of the research community can request additions or other changes to the family by adding an annotation. Anno- tations appear directly on the entry but are attributed to those who have con- tributed them.

External links provide access to many kinds of detailed biological infor- mation stored in other databases and world Wide web resources. For exam- ple, the PAX family entry is linked m the PROSITE database 2, which provides a detailed description of this family and links to members of the family in other organisms. Links can also be made to other resources available on the Web, such as the 'Gene Family Databa~'u~'5~ prototype that contains detailed infor- mation about gene families contributed by members of the research community and hyperlinks to many databases.

Listed citations are hyperlinked to the citation database of the GDB, from which abstracts and other information is avail- able. Gene families are just one example of the detailed biological information to be found in the GDB. Please stop by and look for your favorite gene or gene fam- ily. starting at the GDB homepage 4

Referenc~ and URLs 1 Fasman, K.H., Letovsky, S.I.,

Cottingham, R3.V. and Kingsbury, D.T. (1996) Nucleic Acids Res. 1, 57-63

2 Bairoch, A., Bucher, P. and Hofmann, K (1996) Nucleic Acids Res. 1,189-196

3 htt p://info.gdb.org/~avolt z/home. html

4 htt p://gdbwww.gdb.org

Amy IL Voltz :tvoltz@gdb,org

,lobns Hopkins trrtlit~.r$il| L School of Medicine. Division of Biomedical htforntatiolt Sciences,

2024 E. Monument St, Baltimore, MD 21205. USA.

Genetwork is a regular column of news and information about Intemet resources for researchers in genetics and development. Genetwork is compiled and edited with the help of Steven E. Brenner (MRC Laboratory o f Molecular Biology. Hills Road, Cambridge, UK CB2 2QH), and Jeremy Rashbass (Depar tmem of Histopathology, Addenbrooke ' s Hospital, Hills Road, Cambridge, UK CB2 2QQ).

If you would like to announce o r publicize an I n t e r n e t r e s o u r ~ , please contact: TIC~elsevier.co.uk

TIG JUNE 1996 VOL. 12 NO. 6

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