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.
; 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.
| Patrushev, Ilya; James-Zorn, Christina; Ciau-Uitz, Aldo et al. (2018) New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images. PLoS Comput Biol 14:e1006077 |
| Karimi, Kamran; Wuitchik, Daniel M; Oldach, Matthew J et al. (2018) Distinguishing Species Using GC Contents in Mixed DNA or RNA Sequences. Evol Bioinform Online 14:1176934318788866 |
| Karimi, Kamran; Fortriede, Joshua D; Lotay, Vaneet S et al. (2018) Xenbase: a genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Res 46:D861-D868 |
| James-Zorn, Christina; Ponferrada, Virgilio; Fisher, Malcolm E et al. (2018) Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database. Methods Mol Biol 1757:251-305 |
| Vize, Peter D; Zorn, Aaron M (2017) Xenopus genomic data and browser resources. Dev Biol 426:194-199 |
| Session, Adam M; Uno, Yoshinobu; Kwon, Taejoon et al. (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538:336-343 |
| 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 |
| Deans, Andrew R; Lewis, Suzanna E; Huala, Eva et al. (2015) Finding our way through phenotypes. PLoS Biol 13:e1002033 |
| Vize, Peter D; Liu, Yu; Karimi, Kamran (2015) Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase. Cytogenet Genome Res 145:278-82 |
| Grant, Ian M; Balcha, Dawit; Hao, Tong et al. (2015) The Xenopus ORFeome: A resource that enables functional genomics. Dev Biol 408:345-57 |
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