Ovarian Kaleidoscope Database: Ten Years and Beyond1

ABSTRACT Ovarian Kaleidoscope database (OKdb) is an online, searchable, public database containing text-based and DNA microarray data to facilitate research by ovarian researchers. Using key words and predetermined categories, users can search ovarian gene information based on gene function, cell type of expression, cellular localization, hormonal regulation, mutant phenotypes, chromosomal location, ligand-receptor relationship, and other criteria, either alone or in combination. For individual genes, users can access more than 10 extensive DNA microarray datasets to interrogate gene expression patterns in a development-specific and cell type-specific manner. All ligand and receptor genes expressed in the ovary are matched to facilitate investigation of paracrine/autocrine signaling. More than 3500 ovarian genes in the database are matched to 185 gene pathways in the Kyoto Encyclopedia of Genes and Genomes to allow for elucidation of gene interactions and relationships. In addition to >400 genes with infertility or subfertility phenotypes when mutated in mice or humans, the OKdb also lists ∼50 and ∼40 genes associated with polycystic ovarian syndrome and primary ovarian insufficiency, respectively. The expanding OKdb is updated weekly and allows submission of new genes by ovarian researchers to allow instant access to DNA microarray datasets for newly submitted genes. The present database is a virtual community for ovarian researchers and allows users to instantaneously provide their comments for individual gene pages based on an automated Web-discussion system. In the coming years, we will continue to add new features to serve the ovarian research community.

[1]  B. Zhang,et al.  Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromosome 2p16.3, 2p21 and 9q33.3 , 2011, Nature Genetics.

[2]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[3]  Peter Braude,et al.  Human gene expression first occurs between the four- and eight-cell stages of preimplantation development , 1988, Nature.

[4]  Ronald W Davis,et al.  A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. , 2004, Developmental cell.

[5]  R. Schultz,et al.  Transcript profiling during mouse oocyte development and the effect of gonadotropin priming and development in vitro. , 2005, Developmental biology.

[6]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[7]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[8]  R. Legro,et al.  Molecular progress in infertility: polycystic ovary syndrome. , 2002, Fertility and sterility.

[9]  Juan Carlos Izpisua Belmonte,et al.  Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development , 2011, Development.

[10]  D. Melton,et al.  Nuclear Reprogramming in Cells , 2008, Science.

[11]  C P Leo,et al.  The Ovarian Kaleidoscope database: an online resource for the ovarian research community. , 2000, Endocrinology.

[12]  Cole Trapnell,et al.  Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.

[13]  Fanyi Zeng,et al.  Transcript profiling during preimplantation mouse development. , 2004, Developmental biology.

[14]  Editorial: A New Database for Tissue-Specific Gene Expression and Function in the Ovary. , 2000, Endocrinology.

[15]  Rami Rauch,et al.  Matching receptome genes with their ligands for surveying paracrine/autocrine signaling systems. , 2007, Molecular endocrinology.

[16]  D. Castrillon,et al.  Genomewide Discovery and Classification of Candidate Ovarian Fertility Genes in the Mouse , 2007, Genetics.

[17]  M. Griswold,et al.  Profiling Gene Expression During the Differentiation and Development of the Murine Embryonic Gonad1 , 2005, Biology of reproduction.

[18]  U. Vitt,et al.  Perspective: the ovarian kaleidoscope database-II. Functional genomic analysis of an organ-specific database. , 2002, Endocrinology.

[19]  Fuchou Tang,et al.  mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system. , 2009, Journal of biomolecular techniques : JBT.

[20]  A. Hsueh,et al.  Ovarian brain-derived neurotrophic factor (BDNF) promotes the development of oocytes into preimplantation embryos. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Izhar Ben-Shlomo,et al.  Signaling Receptome: A Genomic and Evolutionary Perspective of Plasma Membrane Receptors Involved in Signal Transduction , 2003, Science's STKE.