Submitted by Chris Mungall on Thu, 03/13/2014 - 11:12
Are you the developer of an enrichment analysis tool, or the do you have a website that makes use of enrichment algorithms? If so, we would like you hear comments on our proposed enrichment analysis API.
The goal is to be able to hook in 3rd party services to the main GO website. The diagram above illustrates the flow.
Submitted by Seth Carbon on Wed, 03/12/2014 - 17:05
We are happy to announce the imminent public release of AmiGO 2, the next generation AmiGO browser for the Gene Ontology and annotations. This release brings many new features to AmiGO, including tremendous speed improvements and greatly improved search functionality. It will be available from tomorrow at the usual place: http://amigo.geneontology.org.
Submitted by Monica Munoz-Torres on Tue, 03/11/2014 - 17:26
The Enrichment Map Cytoscape Plugin allows userts to visualize the results of gene-set enrichment as a network. It will operate on any generic enrichment results as well as specifically on Gene Set Enrichment Analysis (GSEA) results.
Nodes represent gene-sets and edges represent mutual overlap; in this way, highly redundant gene-sets are grouped together as clusters, dramatically improving the capability to navigate and interpret enrichment results.
Submitted by Monica Munoz-Torres on Tue, 03/11/2014 - 17:08
Reconstructing gene regulatory networks from high-throughput data is a long-standing challenge. The Reverse Engineering Assessment and Methods (DREAM) project, performed a comprehensive blind assessment of over 30 network inference methods on Escherichia coli, Staphylococcus aureus, Saccharomyces cerevisiae and in silico microarray data. They characterized the performance, data requirements and inherent biases of different inference approaches, observing that no single inference method performs optimally across all data sets.
Submitted by Chris Mungall on Thu, 02/27/2014 - 17:56
We are pleased to announce an Uberon workshop, satellite of the
Biocuration2014 meeting, to be held in Toronto, Canada, on the 5th and
6th April 2014.
Uberon is an integrated cross-species anatomy ontology, representing a
variety of entities classified according to traditional anatomical
criteria such as structure, function, and developmental
lineage. Uberon provides a necessary bridge between anatomical
structures in different taxa for cross-species inference, allowing
integration of model organism, human, and comparative morphology