Perspective: the ovarian kaleidoscope database-II. Functional genomic analysis of an organ-specific database.
In the postgenomic era, it is now possible to investigate the function of all human genes to provide an integrated view of physiology and pathophysiology. An organ-based approach has been used to set up a database integrating existing text-based literature on individual ovarian genes and their sequence-based data in the GenBank. The Ovarian Kaleidoscope database (OKdb) has accumulated nearly one thousand individual gene pages that are searchable based on gene function, cellular localization, chromosomal position, ovarian cell type, ovarian function, mutant phenotypes, and other criteria. The present review exemplifies the use of this organ-based database in setting up gene pathway maps for DNA array analysis, identifying key gene networks essential for infertility phenotypes, comparing chromosomal synteny regions for finding candidate fertility genes, categorizing cell-specific and hormonally coregulated genes for promoter analysis, and documenting potential ligands and receptors in the paracrine regulation of follicular development. The present global analysis of gene function and relationships in an organ-specific manner provides a functional genomic paradigm for the future understanding of the physiology and pathophysiology of diverse organs.
Ben-Shlomo
Izhar
I
Division of Reproductive Biology, Department of Gynecology and Obstetrics, Stanford University School of Medicine, Stanford, California 94305-5317, USA.
Vitt
Ursula A
UA
Hsueh
Aaron J W
AJ
D000818:Animals; D002875:Chromosomes / Q000235:genetics / Q000648:ultrastructure; D016208:Databases, Factual; D005260:Female; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D007247:Infertility, Female / Q000235:genetics; D008967:Molecular Biology; D010053:Ovary / Q000502:physiology*; D019899:Paracrine Communication / Q000235:genetics / Q000502:physiology; D011401:Promoter Regions, Genetic