Check out our new tissue enrichment analysis tool!

We are pleased to announce our new web-based tool ‘TEA‘, this tool has been developed for identifying enrichment of C. elegans tissues among gene sets.  The software is also available for download.  Description of the tool is published here.

Latest chapter of WormBook in GENETICS: Programmed Cell Death During Caenorhabditis elegans Development

Check out the latest chapter of WormBook in GENETICS!

Programmed Cell Death During Caenorhabditis elegans Development
Barbara Conradt, Yi-Chun Wu, Ding Xue
GENETICS August 1, 2016 vol. 203 no. 4 1533-1562; DOI: 10.1534/genetics.115.186247

Programmed cell death is an integral component of Caenorhabditis elegans development. Genetic and reverse genetic studies in C. elegans have led to the identification of many genes and conserved cell death pathways that are important for the specification of which cells should live or die, the activation of the suicide program, and the dismantling and removal of dying cells. Molecular, cell biological, and biochemical studies have revealed the underlying mechanisms that control these three phases of programmed cell death. In particular, the interplay of transcriptional regulatory cascades and networks involving multiple transcriptional regulators is crucial in activating the expression of the key death-inducing gene egl-1 and, in some cases, the ced-3 gene in cells destined to die. A protein interaction cascade involving EGL-1, CED-9, CED-4, and CED-3 results in the activation of the key cell death protease CED-3, which is tightly controlled by multiple positive and negative regulators. The activation of the CED-3 caspase then initiates the cell disassembly process by cleaving and activating or inactivating crucial CED-3 substrates; leading to activation of multiple cell death execution events, including nuclear DNA fragmentation, mitochondrial elimination, phosphatidylserine externalization, inactivation of survival signals, and clearance of apoptotic cells. Further studies of programmed cell death in C. elegans will continue to advance our understanding of how programmed cell death is regulated, activated, and executed in general.

WormBase will be at the TAGC in Orlando!

WormBase will be at the The Allied Genetics Conference 2016 (TAGC), July 13-17, 2016, in Orlando, Florida.  WormBase will have posters, will be hosting workshops and will have a Demo booth together with other model organism databases.  This is your opportunity to ask questions related to data and querying it, in WormBase and other databases. There will be a limited number of free goodies distributed to visitors at the booth.  So get to the WormBase booth as fast as you can!

Announcing the Alliance of Genome Resources

An Alliance of Genome Resources has been formed to provide better support for the biological sciences via an integration of shared data, standardization of data models and interfaces, and unified outreach to researchers, educators and the public. The initial members of the Alliance are the Gene Ontology Consortium and six model organism databases: Saccharomyces Genome Database, WormBase, FlyBase, Zebrafish Model Organism Database, Mouse Genome Database and Rat Genome Database. The integration of these projects will not decrease the types of data, tools and community support that are currently provided by these resources but rather will provide the best displays and tools currently in use and allow us to efficiently develop new tools in a collaborative manner. As we move toward deeper integration of our content and software we will provide easy-to-use cross-organism queries of the extensive data available in the component resources. Also, future integration of other resources will benefit all biologists.

The Alliance of Genome Resources will continue the tradition of these community resources by enabling researchers to leverage the published results and datasets from well-studied organisms for their daily research. By integrating high-quality expertly curated information, the Alliance will continue to provide researchers access to data, information and knowledge found in published and publicly available sources that would require many lifetimes to assemble.

The modular architecture of modern websites will allow the Alliance to maintain the uniqueness of each research community – and each user – through customization. We will present a common view of information whenever possible. A common website will have distinct entry points for the different communities and tools that will maintain the community-building features of our current resources. By joining the Alliance of Genome Resources, the member organizations pledge mutual support, as well as support of research communities having interests in common with those of the Alliance, with the goal of delivering facile information retrieval for all biologists. We will definitely need your support in obtaining sufficient funding for these efforts.