Animal models provide powerful experimental tools to test gene function and interrogate biological pathways. Comparative functional genomics between humans and model organisms has led to a wealth of discoveries, and it is clear that this will continue to play an important role in unlocking the potential of the genome for human health. In this post genomic era highly annotated and easily accessible data are increasingly essential for researchers to integrate vast amounts of sequence, expression and functional data into a meaningful biological synthesis. The goal of this proposal is to maintain and enhance Xenbase;the Xenopus model organism database. The African frogs Xenopus has long been one of the premiere model organisms used by cell and developmental biologists, providing numerous fundamental insights. The large and abundant Xenopus embryos enable sophisticated embryology, easy manipulation of gene expression by microinjection and biochemical analyses. Together with recent advances in genome and EST sequencing, the generation of full-length cDNA sets, microarray analysis, functional genomics screens, gene knockdown using anitsense morpholino oligos, the development of rapid transgenics and the establishment of Xenbase has made Xenopus a powerful system for functional genomics. Xenbase is a comprehensive database that provides a portal to inter-related Xenopus data including genomic, mRNA and protein sequence, gene expression, function and publications, which is all highly integrated with NCBI and other model organism databases. The goal of this proposal is to maintain and expand Xenbase.
Aim 1) Maintain and further curate the data in Xenbase by implementing Testpresso data mining and manual curation.
Aim 2) Enhance Xenbase functionality by introducing morpholino and mutant phenotypes.
Aim 3) Support new content on Xenbase gene pages including mRNA splicing microarrays, and a Xenopus WIKI.
Aim 4) Continue and expand collaborative research and service efforts by further integrating Xenbase data with NCBI and other model organism data bases. This proposal will empower Xenopus research and provide the broader scientific community a means of accessing a wealth of Xenopus data.

Public Health Relevance

; The Xenopus model system is a powerful tool for testing gene function in vivo. As gene functions are widely conserved between vertebrates data from Xenopus can be used to predict a genes role in human health and disease. This proposal to maintain and enhance Xenbase: will provide sophisticated bioinformatics tools allowing biomedical researchers to link Xenopus functional genomics data to human genes.

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Biotechnology Resource Grants (P41)
Project #
5P41HD064556-03
Application #
8292203
Study Section
Special Emphasis Panel (ZHD1-MRG-C (41))
Program Officer
Coulombe, James N
Project Start
2010-06-01
Project End
2015-05-31
Budget Start
2012-06-01
Budget End
2013-05-31
Support Year
3
Fiscal Year
2012
Total Cost
$843,528
Indirect Cost
$192,603
Name
Cincinnati Children's Hospital Medical Center
Department
Type
DUNS #
071284913
City
Cincinnati
State
OH
Country
United States
Zip Code
45229
Karpinka, J Brad; Fortriede, Joshua D; Burns, Kevin A et al. (2015) Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. Nucleic Acids Res 43:D756-63
Karimi, Kamran; Vize, Peter D (2014) The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud. Database (Oxford) 2014:
Bowes, Jeff B; Snyder, Kevin A; James-Zorn, Christina et al. (2013) The Xenbase literature curation process. Database (Oxford) 2013:bas046
James-Zorn, Christina; Ponferrada, Virgilio G; Jarabek, Chris J et al. (2013) Xenbase: expansion and updates of the Xenopus model organism database. Nucleic Acids Res 41:D865-70
Brady, Aisling K; Snyder, Kevin A; Vize, Peter D (2011) Circadian cycles of gene expression in the coral, Acropora millepora. PLoS One 6:e25072
McCoy, Kyle E; Zhou, Xiaolan; Vize, Peter D (2011) Non-canonical wnt signals antagonize and canonical wnt signals promote cell proliferation in early kidney development. Dev Dyn 240:1558-66