The Vertebrate Genome Annotation (Vega) database

Ashurst, Jennifer

doi:10.1093/nar/gki135

Cited by 131 publications

(116 citation statements)

References 33 publications

(15 reference statements)

Supporting

Mentioning

113

Contrasting

Unclassified

Order By: Relevance

“…Finally, we estimate that the CS/TS ratio of true sites (IPAS) should be close to that observed in a reliable set of transcript 39-ends, such as H-inv full-length cDNAs (Imanishi et al 2004) or the VEGA database (Ashurst et al 2005). CS/TS is 0.67 in H-inv2 and 0.63 in VEGA.…”

Section: Measure Of Fpas Ipas and Gpas Based On Cs/ts Ratiosupporting

confidence: 54%

See 1 more Smart Citation

The disparate nature of “intergenic” polyadenylation sites

Lopez

Granjeaud²,

Ara³

et al. 2006

RNA

View full text Add to dashboard Cite

The termination of mature eukaryotic mRNAs occurs at specific polyadenylation sites located downstream from stop codons in the 39-untranslated region (UTR). An accurate delineation of these sites is essential for the study of 39-UTR-based gene regulation and for the design of pertinent probes for transcriptome analysis. Although typical poly(A) sites are located between 0 and 2 kb from the stop codon, EST sequence analyses have identified sites located at unexpectedly long ranges (5-10 kb) in a number of genes. Here we perform a complete mapping of EST and full-length cDNA sequences on the mouse and human genome to observe putative poly(A) sites extending beyond annotated 39-ends and into the intergenic regions. We introduce several quality parameters for poly(A) site prediction and train a classification tree to associate P-values to predicted sites. We observe a higher than background level of high-scoring sites up to 12-15 kb past the stop codon, both in human and mouse. This leads to an estimate of about 5000 human genes having unreported 39-end extensions and about 3500 novel polyadenylated transcripts lying in present ''intergenic'' regions. These high-scoring, long-range poly(A) sites corresponding to novel transcripts and gene extensions should be incorporated into current human and mouse gene repositories.

show abstract

Section: Measure Of Fpas Ipas and Gpas Based On Cs/ts Ratiosupporting

confidence: 54%

“…As a control, we used 4674 poly(A) sites from the VEGA database of known transcripts (Ashurst et al 2005), as a training set for Class 1. We obtained similar ratios of reclassified sites as with our initial training set (data not shown).…”

Section: Classifying and Scoring Poly(a) Sitesmentioning

confidence: 99%

The disparate nature of “intergenic” polyadenylation sites

Lopez

Granjeaud²,

Ara³

et al. 2006

RNA

View full text Add to dashboard Cite

show abstract

“…We found that the 59 and 39 halves did not differ significantly ( Figure S2B). In addition, we tried restricting our analysis to 627 genes whose transcription start site is annotated in the Vertebrate Genome Annotation (Vega) database [20], which is manually annotated. The results for this subset did not differ from those for the whole set of genes ( Figure S2C).…”

Section: Resultsmentioning

confidence: 99%

Selective constraint on noncoding regions of hominid genomes

Bush¹,

Lahn²

2005

PLoS Comp Biol

View full text Add to dashboard Cite

An important challenge for human evolutionary biology is to understand the genetic basis of human-chimpanzee differences. One influential idea holds that such differences depend, to a large extent, on adaptive changes in gene expression. An important step in assessing this hypothesis involves gaining a better understanding of selective constraint on noncoding regions of hominid genomes. In noncoding sequence, functional elements are frequently small and can be separated by large nonfunctional regions. For this reason, constraint in hominid genomes is likely to be patchy. Here we use conservation in more distantly related mammals and amniotes as a way of identifying small sequence windows that are likely to be functional. We find that putatively functional noncoding elements defined in this manner are subject to significant selective constraint in hominids.

show abstract

“…Computational pipelines such as that run by Ensembl [1] provide automated annotation of most protein-coding genes, which for some genomes have been augmented by manual curation to improve the accuracy and completeness of gene sets: examples of this approach include the Vega database of vertebrate annotation [2] and some popular model organism databases such as Wormbase [3] and FlyBase [4].…”

Section: Introductionmentioning

confidence: 99%

Large Scale Discovery of Promoter Motifs in Drosophila melanogaster

Down¹,

Bergman²,

Su³

et al. 2005

PLoS Comput Biol

View full text Add to dashboard Cite

A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs) that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

show abstract

The Vertebrate Genome Annotation (Vega) database

Cited by 131 publications

References 33 publications

The disparate nature of “intergenic” polyadenylation sites

The disparate nature of “intergenic” polyadenylation sites

Selective constraint on noncoding regions of hominid genomes

Large Scale Discovery of Promoter Motifs in Drosophila melanogaster

Contact Info

Product

Resources

About