The mouse Gene Expression Database (GXD): 2019 update

Abstract

The mouse Gene Expression Database (GXD) is an extensive, well-curated community resource freely available at www.informatics.jax.org/expression.shtml. Covering all developmental stages, GXD includes data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments in wild-type and mutant mice. GXD’s gene expression information is integrated with the other data in Mouse Genome Informatics and interconnected with other databases, placing these data in the larger biological and biomedical context. Since the last report, the ability of GXD to provide insights into the molecular mechanisms of development and disease has been greatly enhanced by the addition of new data and by the implementation of new web features. These include: improvements to the Differential Gene Expression Data Search, facilitating searches for genes that have been shown to be exclusively expressed in a specified structure and/or developmental stage; an enhanced anatomy browser that now provides access to expression data and phenotype data for a given anatomical structure; direct access to the wild-type gene expression data for the tissues affected in a specific mutant; and a comparison matrix that juxtaposes tissues where a gene is normally expressed against tissues, where mutations in that gene cause abnormalities.

Convergent vomeronasal system reduction in mammals coincides with convergent losses of calcium signalling and odorant‐degrading genes

“…Tmprss11g and Kcnmb3 both show lower expression levels in VNO and olfactory epithelium when compared to genes of the same family (Figure ). Ubqln5 is very lowly expressed in VNO or olfactory epithelium (Figure ) but shows an olfactory epithelium‐specific expression during mouse embryonic development (E15) based on in situ hybridization data (GDX: MGI:1918230; Diez‐Roux et al, ; Smith et al, ). Among the candidate genes, Ubqln5 exhibits the highest expression in testis (Figure ).…”

Axin-mediated regulation of lifespan and muscle health inC. elegansinvolves AMPK-FOXO signaling

“…Interestingly, constitutive activation of pry-1 in muscles but not hypodermis was found to be beneficial to animals. Such a role of pry-1 does not appear to be unique to C. elegans since Axin homologs in other eukaryotes are also expressed in muscles (Smith et al, 2019;Uhlén et al, 2015). Moreover, we found that mAxin1 was able to extend the lifespan of C. elegans when ectopically expressed in the muscle tissue.…”

“…Interestingly, muscle-specific expression of mouse Axin (mAxin1) in C. elegans also extended the lifespan of animals, suggesting that Axin's role in aging may be conserved. It is worth mentioning that Axin is known to be expressed in mouse and human skeletal muscles (Smith et al, 2019;Uhlén et al, 2015). Our molecular genetic experiments revealed that PRY-1's role in aging depends on AAK-2 and DAF-16.…”

Genetic architecture underlying changes in carotenoid accumulation during the evolution of the Blind Mexican cavefish,Astyanax mexicanus

“…GTF2I is a general transcription factor that is ubiquitously expressed. DTX2 is an E3 ubiquitin ligase that acts as a positive regulatory of Notch signaling (Matsuno, Diederich, Go, Blaumueller, & Artavanis-Tsakonas, 1995) and is expressed in the mouse and human gastrointestinal (GI) tract (Smith et al, 2019)(GTEx Analysis Release V8 (dbGaP Accession phs000424.v8.p2)). Considering that Notch activity promotes the formation of absorptive cells in the GI tract (Tian et al, 2015) we compared surface fish and Pachón cavefish DTX2 using the available annotations for the surface fish and Pachón cavefish genomes ( Figure 5A).…”