5.6 Species-Specific Databases 117
genes and proteins of this yeast from the scientific literature, and presents
this information on individual Locus pages for each yeast gene. The Pathway
Tools software (Karp et al. 2002a) and the MetaCyc Database of metabolic
reactions (Karp et al. 2002b) were used to generate the metabolic pathway
information forS. cerevisiae. Metabolic pathways are illustrated in graphical
format and the information can be viewed at multiple levels, ranging from
general summaries to detailed diagrams showing each compound’s chem-
ical structure. Enzymatic activities of the proteins shown in each pathway
diagram are linked to the corresponding SGD Locus pages.
FlyBase flybase.bio.indiana.edu
The fruit fly,Drosophila melanogaster, is one of the most studied eukaryotic or-
ganisms and a central model for the Human Genome Project (FlyBase 2002).
FlyBase is a comprehensive database containing information on the genetics
and molecular biology ofDrosophila. It includes data from theDrosophilage-
nome projects and data curated from the literature. FlyBase is a joint project
with the BerkeleyDrosophilaGenome Project.
FlyBase is one of the founding participants in the GO consortium. As an
example of how FlyBase is related to GO, consider theD. melanogastergene
p53 (FlyBase ID: FBgn0039044). Through FlyBase GO annotations, we can
learn that p53 is classified by the organization principles as follows:
- GO:Molecular function:The p53 gene encodes a DNA-binding protein prod-
uct which functions as a transcription factor for RNA polymerase II. - GO:Biological process:We can also learn that p53 is involved in important
molecular processes such as DNA damage response, apoptosis, and re-
sponse to radiation. - GO:Cellular component:Lastly, we find that the p53 protein is located in
the nucleus.
Besides these GO annotations, we can also learn from the FlyBase report that
the p53 gene is expressed not only in adult flies, but also during oogenesis
(including nurse cell and oocyte) and during the embryonic stage (includ-
ing embryonic/larval foregut, embryonic/larval hindgut, embryonic/larval
midgut, germ cell, and mesoderm).
MGD http://www.informatics.jax.org
The Mouse Genome Database at the Jackson Laboratory in Bar Harbor, Maine,
is a resource for mouse genome information. The human-mouse synteny
(i.e., the comparison of the two mammalian organisms) provides important