rVista for comparative sequence-based discovery of functional transcription factor binding sites.

By Gabriela G. Loots, Ivan Ovcharenko, Lior S. Pachter, Inna Dubchak, Edward M. Rubin. Genome Research, 2002

462 citations recorded by the source corpus.

Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVista, for high-throughput discovery of cis-regulatory elements that combines clustering of predicted transcription factor binding sites (TFBSs) and the analysis of interspecies sequence conservation to maximize the identification of functional sites. To assess the ability of rVista to discover true positive TFBSs while minimizing the prediction of false positives, we analyzed the distribution of several TFBSs across 1 Mb of the well-annotated cytokine gene cluster (Hs5q31; Mm11). Because a large number of AP-1, NFAT, and GATA-3 sites have been experimentally identified in this interval, we focused our analysis on the distribution of all binding sites specific for these transcription factors. The exploitation of the orthologous human-mouse dataset resulted in the elimination of > 95% of the approximately 58,000 binding sites predicted on analysis of the human sequence alone, whereas it identified 88% of the experimentally verified binding sites in this region.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cc0478afc6d43847352906c2e2834c639f83d9a4

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Citations in the corpus

Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence (2003, background): “There are Web sites that provide these services, e.g., PipMaker ( UNIT 10.2; Schwartz et al., 2000) or rVista (Loots et al., 2002).”
ConSite: web-based prediction of regulatory elements using cross-species comparison (2004, methodology): “Besides the intuitive interface design, ConSite integrates several features not found in other TFBS prediction services such as TESS (17) or rVista (18).”
Computational prediction of transcription-factor binding site locations (2003, methodology): “The program rVISTA performs global alignment of genomic sequences and then searches within the conserved regions for conserved TFBSs matching known PWMs [32].”
Transcriptional regulation by calcium, calcineurin, and NFAT. (2003, background): “These regions often (but not always) correspond to highly conserved noncoding sequences (CNS) identified by comparing the sequences of gene loci in two or more mammalian genomes using Web-based programs such as VISTA (Mayor et al. 2000; Loots et al. 2002; Bray et al. 2003) or PipMaker (Schwartz et a”
Identification of conserved regulatory elements by comparative genome analysis (2003, background): “The only similarly scoped resource is the recently published rVista [33], which searches for TFBSs in a reference sequence and filters the results for sites in regions of high conservation with respect to a second genomic sequence.”
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes (2004, methodology): “A dynamic Picture (23) conservation plot, a portal to the rVista tool (24), an alignment dot-plot and a tool for dynamic annotation of ECRs in the alignment are also automatically provided.”
The Diploid Genome Sequence of an Individual Human (2007, background): “These genomic datasets have also enabled the identification of additional functional sequence such as cis-regulatory DNA [24–29] as well as both noncoding and microRNA [30–34] .”
The State of the Art of Mammalian Promoter Recognition (2003, background): “As discussed above, such comparative approaches are also applicable to promoters.(28) However, since, in particular, first non-coding exons and intron sequences are often much less conserved than coding exons, in silico promoter recognition will be important to ensure that promoter sequences are bei”
rVISTA 2.0: evolutionary analysis of transcription factor binding sites (2004, methodology): “We have previously shown that the rVista tool combines pattern recognition with comparative sequence analysis to dramatically reduce the number of false positive TFBS matches and enrich for functional sites (5).”
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes (2005, background): “Other resources are available for detecting and visualizing binding sites within the conserved regions of human genes [Consite (11), rVISTA (38), dbTSS (39), CONREAL (40), CORG (41)], as well as for identifying statistically over-represented motifs in the promoters of related sequences [Clover (42),”
VISTA: computational tools for comparative genomics (2004, methodology): “…searches with comparative sequence analysis reduces the number of predicted transcription factor binding sites by several orders of magnitude (9). rVISTA makes predictions based on using the Match TM program (33) and the TRANSFAC Professional library or user-submitted matrices to identify…”
Serum response factor: toggling between disparate programs of gene expression. (2003, background): “rVISTA and other programs are available to assess conserved modules and clusters of cis-elements important in gene transcription [180,181].”