The Vertebrate Genome Annotation (Vega) database

By J. Ashurst, C.-K. Chen, J. Gilbert, K. Jekosch, S. Keenan, Patrick Meidl, S. Searle, J. Stalker, R. Storey, S. Trevanion and 2 more. Nucleic Acids Res., 2004

394 citations recorded by the source corpus.

The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) has been designed to be a community resource for browsing manual annotation of finished sequences from a variety of vertebrate genomes. Its core database is based on an Ensembl-style schema, extended to incorporate curation-specific metadata. In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences. In addition, it is also possible to view various finished regions from other vertebrates, including mouse and zebrafish. Vega displays only manually annotated gene structures built using transcriptional evidence, which can be examined in the browser. Attempts have been made to standardize the annotation procedure across each vertebrate genome, which should aid comparative analysis of orthologues across the different finished regions.

Subfields: Molecular Biology, Plant Science

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Citations in the corpus

Ensembl 2007 (2006, methodology): “The EGASP gene prediction competition (22) was held to compare a variety of automatic gene prediction methods with a curated and experimentally validated human gene set generated by the Sanger Havana group (3) as part of the Gencode consortium (23).”
Ensembl 2013 (2012, methodology): “We update the human gene set for every Ensembl release via a merge of the Ensembl evidence-based automatic annotation and Havana manual annotation (14) to produce an updated GENCODE gene set (9,15).”
Ensembl 2016 (2015, methodology): “Computationally annotated mouse gene annotation is currently merged every release with manual annotation from the HAVANA project (19).”
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. (2007, methodology): “Displayed peaks correspond to a P-value of 10 25, after using the Benjamini-Hochberg correction to adjust for multiple tests (Benjamini and Hochberg 1995).”
Ensembl 2012 (2011, methodology): “These annotations are a merged gene set consisting of the output of the Ensembl evidence-based automatic pipeline (21) and the manual annotation from the Havana project (22).”
UniProt Knowledgebase: a hub of integrated protein data (2011, background): “Ensembl also includes manually curated genes from the Vertebrate Genome Annotation (VEGA) database (11) which is particularly suited to annotation of splice variants which may be missed by automatic pipelines.”
An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex (2014, background): “, 2012), Vega (Ashurst et al., 2005), and AceView (Thierry-Mieg and Thierry-Mieg, 2006) databases (data not shown).”
GENCODE: The reference human genome annotation for The ENCODE Project (2012, methodology): “All genes and pseudogenes within the release have stable Ensembl (ENS) identifications and the manual annotated genes have additional Vega (OTT) IDs (Wilming et al. 2008).”
Ensembl’s 10th year (2009, neutral): “Some of these projects include the Genome Browser at UCSC (1), the databases and resources of the NCBI (2), the Rat Genome Database (RGD) (3) and VEGA (4).”
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. (2009, background): “2008); and (4) the WTSI Vertebrate Genome Annotation (Vega) Genome Browser (Ashurst et al. 2005).”
Ensembl 2009 (2008, methodology): “Ensembl, together with the Sanger Institute HAVANA group (19), is part of multiple collaborations to refine the human geneset including the CCDS (Consensus Coding Sequence) consortium, with RefSeq at NCBI (20) andUCSC (1), and the new ENCODE scale-up project GENCODE (http://www.”
The UCSC Genome Browser (2003, neutral): “…consistently annotated core set of human protein-coding genes obtained from the CCDS project and identified by consensus among the Ensembl, Vega (Wilming et al., 2008), and RefSeq gene annotation sets; and the GENCODE Genes track, showing high-quality manual annotations merged with…”
The IMGT/HLA database (2008, background): “The cross-references to the IMGT/ HLA database are also included in ENSEMBL (33) and vertebrate genome annotation (VEGA) entries (34).”
Combined Evidence Annotation of Transposable Elements in Genome Sequences (2005, background): “By contrast, recent advances in the field of gene annotation indicate that high-quality gene models can be produced by combining multiple independent sources of computational evidence [4–9].”
Ensembl 2014 (2013, methodology): “We update the human gene set for every Ensembl release via a merge of the Ensembl evidence-based automatic annotation and Havana (14) manual annotation to produce an updated GENCODE gene set.”
The yak genome and adaptation to life at high altitude (2012, background): “…in gene structure on subsequent evolutionary rate analyses, we mapped all the human protein-coding genes from RefSeq 64 , KnownGene 65 and VEGA 66 to each of the other species via their syntenic alignments, then passed the resulting blocks through a series of rigorous filters that selected…”