Database of queryable gene expression patterns for <i>Xenopus</i>

Gilchrist, Michael J.; Christensen, Mikkel; Bronchain, Odile; Brunet, Frédéric; Chesneau, Albert; Fenger, Ursula; Geach, Timothy J.; Ironfield, Holly; Kaya, Ferdinand; Kricha, Sadia; Lea, Robert; Massé, Karine; Néant, Isabelle; Paillard, Elodie; Parain, Karine; Perron, Muriel; Sinzelle, Ludivine; Souopgui, Jacob; Thuret, Raphaël; Ymlahi-Ouazzani, Qods; Pollet, Nicolas

doi:10.1002/dvdy.21940

Cited by 18 publications

(11 citation statements)

References 28 publications

(25 reference statements)

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“…This is used by the e-Mouse Atlas of Gene Expression (EMAGE) [ 19 ] (as described in [ 35 ]) and Allen Developing Mouse Brain Atlas [ 34 ] (as described in [ 36 ]). (c) A third approach, used by XenMARK [ 37 ], relies on a manual annotation process in which specimen expression patterns are drawn onto stage-specific schematic diagrams [ 38 ]. This method avoids the computational complexity of spatial warping, but allows spatial searches from the schematics.…”

Section: Resultsmentioning

confidence: 99%

Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design

Clarkson

2016

BMC Dev Biol

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BackgroundA large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis. As these community resources continue to evolve, it is important to understand how representations of anatomy can facilitate the sharing and integration of data. In addition, attention to the design of the interfaces is critical to make online resources useful and usable.ResultsI first present a survey of online atlases and gene expression resources for model organisms, with a focus on methods of semantic and spatial representation of anatomy. A total of 14 anatomical atlases and 21 gene expression resources are included. This survey demonstrates how choices in semantic representation, in the form of ontologies, can enhance interface search functions and provide links between relevant information. This survey also reviews methods for spatially representing anatomy in online resources. I then provide a collection of patterns for interface design based on the atlases and databases surveyed. These patterns include methods for displaying graphics, integrating semantic and spatial representations, organizing information, and querying databases to find genes expressed in anatomical structures.ConclusionsThis collection of patterns for interface design will assist biologists and software developers in planning the interfaces of new atlases and databases or enhancing existing ones. They also show the benefits of standardizing semantic and spatial representations of anatomy by demonstrating how interfaces can use standardization to provide enhanced functionality.

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Section: Resultsmentioning

confidence: 99%

Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design

Clarkson

2016

BMC Dev Biol

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“…Surprisingly, out of the 174 miRNAs tested 140 showed expression in the developing embryo at some stage. Selected photos showing expression of specific miRNAs can be freely accessed using XenMARK [ 26 ] and Xenbase [ 25 , 32 ]. In Xenbase each miRNA is listed by name (ie miR-206) and clearly states at which stages of development expression is seen.…”

Section: Resultsmentioning

confidence: 99%

“…In this paper we present the expression patterns of 180 miRNAs in Xenopus laevis. These have been made freely available and can be accessed using the XenMARK and Xenbase websites [ 25 , 26 ]. In addition we have carried out small RNA sequencing of Xenopus laevis embryonic tissue.…”

Section: Introductionmentioning

confidence: 99%

A Database of microRNA Expression Patterns in Xenopus laevis

et al. 2015

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MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAs we have looked at show expression in the heart. Our results have been made freely available as a resource in both XenMARK and Xenbase.

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“…A complementary gene expression tool called XenMARK is also available on the web [35]. XenMARK uses an ontology-free annotation system that displays expression images as heat map diagrams projected on embryo schematics.…”

Section: Resultsmentioning

confidence: 99%

Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase

et al. 2013

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BackgroundThe African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying human disease. The Xenopus Anatomy Ontology (XAO) reflects the anatomy and embryological development of Xenopus. The XAO provides consistent terminology that can be applied to anatomical feature descriptions along with a set of relationships that indicate how each anatomical entity is related to others in the embryo, tadpole, or adult frog. The XAO is integral to the functionality of Xenbase (http://www.xenbase.org), the Xenopus model organism database.ResultsWe significantly expanded the XAO in the last five years by adding 612 anatomical terms, 2934 relationships between them, 640 synonyms, and 547 ontology cross-references. Each term now has a definition, so database users and curators can be certain they are selecting the correct term when specifying an anatomical entity. With developmental timing information now asserted for every anatomical term, the ontology provides internal checks that ensure high-quality gene expression and phenotype data annotation. The XAO, now with 1313 defined anatomical and developmental stage terms, has been integrated with Xenbase expression and anatomy term searches and it enables links between various data types including images, clones, and publications. Improvements to the XAO structure and anatomical definitions have also enhanced cross-references to anatomy ontologies of other model organisms and humans, providing a bridge between Xenopus data and other vertebrates. The ontology is free and open to all users.ConclusionsThe expanded and improved XAO allows enhanced capture of Xenopus research data and aids mechanisms for performing complex retrieval and analysis of gene expression, phenotypes, and antibodies through text-matching and manual curation. Its comprehensive references to ontologies across taxa help integrate these data for human disease modeling.

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Database of queryable gene expression patterns for Xenopus

Cited by 18 publications

References 28 publications

Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design

Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design

A Database of microRNA Expression Patterns in Xenopus laevis

Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase

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