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Genesis 2012 Mar 01;503:186-91. doi: 10.1002/dvg.20811.
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Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks.

Beer R , Wagner F , Grishkevich V , Peshkin L , Yanai I .

The availability of both the Xenopus tropicalis genome and the soon to be released Xenopus laevis genome provides a solid foundation for Xenopus developmental biologists. The Xenopus community has presently amassed expression data for ∼2,300 genes in the form of published images collected in the Xenbase, the principal Xenopus research database. A few of these genes have been examined in both X. tropicalis and X. laevis and the cross-species comparison has been proven invaluable for studying gene function. A recently published work has yielded developmental expression profiles for the majority of Xenopus genes across fourteen developmental stages spanning the blastula, gastrula, neurula, and the tail-bud. While this data was originally queried for global evolutionary and developmental principles, here we demonstrate its general use for gene-level analyses. In particular, we present the accessibility of this dataset through Xenbase and describe biases in the characterized genes in terms of sequence and expression conservation across the two species. We further indicate the advantage of examining coexpression for gene function discovery relating to developmental processes conserved across species. We suggest that the integration of additional large-scale datasets--comprising diverse functional data--into Xenbase promises to provide a strong foundation for researchers in elucidating biological processes including the gene regulatory programs encoding development.

PubMed ID: 21956895
PMC ID: PMC8128080
Article link: Genesis
Grant support: [+]

Species referenced: Xenopus tropicalis Xenopus laevis
Genes referenced: acod1lb admp b3dm27 bix1.1 bix1.2 btg5.3 cdx1 foxi4.2 gbx2 gbx2.2 gdf3 gs17 gsc hesx1 mixer neurog1 neurog2 neurog3 nodal3.1 nog nog2 phyhdlb pou5f3 sbk1 sbk1l sbk1l2 slc30a8 stx19 tmem150b XB22062454

Article Images: [+] show captions
References [+] :
Bowes, Xenbase: gene expression and improved integration. 2010, Pubmed, Xenbase