XB-ART-44185Genesis March 1, 2012; 50 (3): 186-91.
Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks.
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
Article link: Genesis
Genes referenced: neurog1 gs17 slc30a8 stx19 loc100490918 btg5.3 sbk1 tmem150b b3dm27 loc101730250 sbk1l acod1 admp bix1.1 bix1.2 cdx1 foxi4.2 gbx2.1 gbx2.2 gdf3 gsc hesx1 mixer neurog2 neurog3 nodal3.1 nog nog2 pou5f3.1 sbk1l2
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|Figure 1. Identity between the coding sequences of Xenopus laevis and Xenopus tropicalis (light grey) and between Xenopus laevis paralogs (dark grey). Sequence identity was determined using blastn between the 11,095 pairs of the previously delineated orthologs (Yanai et al.,2011). Pairs of X. laevis paralogs were retrieved from a recent study (Hellsten et al.,2007) and compared as for the orthologs. Reproduced with permission of the Publisher, John Wiley & Sons|
|Figure 2. Comparative gene expression profiles across Xenopuslaevis and Xenopustropicalis. a. In situ gene expression comparison for neurog1 as determined in Nieber et al. (2009). Numbers indicate developmental stages. Top row is X. tropicalis. This image is taken from (Nieber et al.,2009). b. Gene expression comparison from the developmental time-course microarray data (Yanai et al.,2011). Fourteen stages were sampled and the units of expression are in log10 scale. c,d. Expression profiles for noggin and noggin2 in the same format as b. Reproduced with permission of the Publisher, John Wiley & Sons.|
|Figure 3. Biases of Xenopus research towards genes with higher conservation of sequence and expression. a. Genes with Xenbase expression images as a function of their sequence similarity. The plot indicates the fraction of genes with expression images in Xenbase for the shown sequence similarity ranges. b. Genes with Xenbase expression images as a function of their expression similarity. Expression divergences between X. laevis and X. tropicalis (Yanai et al.,2011) were sorted and split into equally populated bins. The fraction of genes in each bin with Xenbase images is shown. Reproduced with permission of the Publisher, John Wiley & Sons.|
|Figure 4. Clustering of comparative gene expression profiles. a. Each plot indicates a plot of genes clustered by Heyer clustering as presented previously (Yanai et al.,2011). The clustering was performed only on X. laevis profiles. Four expression clusters are shown. The unbroken lines correspond to the X. laevis profiles while the dashed lines show the superimposed X. tropicalis profiles. The full clustering is provided in Supporting Information Table S1. Reproduced with permission of the Publisher, John Wiley & Sons.|