RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.
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RSAT variation-tools: An accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding.

Santana-Garcia, Walter;Rocha-Acevedo, Maria;Ramirez-Navarro, Lucia;Mbouamboua, Yvon;Thieffry, Denis;Thomas-Chollier, Morgane;Contreras-Moreira, Bruno;van Helden, Jacques;Medina-Rivera, Alejandra;
computational and structural biotechnology journal 2019 Vol. 17 pp. 1415-1428
225
santanagarcia2019rsatcomputational

Abstract

Gene regulatory regions contain short and degenerated DNA binding sites recognized by transcription factors (TFBS). When TFBS harbor SNPs, the DNA binding site may be affected, thereby altering the transcriptional regulation of the target genes. Such regulatory SNPs have been implicated as causal variants in Genome-Wide Association Study (GWAS) studies. In this study, we describe improved versions of the programs designed to predict regulatory variants, and present four case studies to illustrate their usage and applications. In brief, facilitate i) obtaining variation information, ii) interconversion of variation file formats, iii) retrieval of sequences surrounding variants, and iv) calculating the change on predicted transcription factor affinity scores between alleles, using motif scanning approaches. Notably, the tools support the analysis of haplotypes. The tools are included within the well-maintained suite Regulatory Sequence Analysis Tools (RSAT, http://rsat.eu), and accessible through a web interface that currently enables analysis of five metazoa and ten plant genomes. can also be used in command-line with any locally-installed Ensembl genome. Users can input personal collections of variants and motifs, providing flexibility in the analysis.

Keywords

snps transcription factors binding motifs ceu, northern europeans from utah crm, cis-regulatory module gwas, genome wide association studies ld, linkage disequilibrium mpra, massively parallel reporter assays: mpra pssm, position specific scoring matrix position specific scoring matrix roc, receiver operating characteristic rsat, regulatory sequence analysis tools regulatory variants snp, single nucleotide polymorphism sois, snps of interest tf, transcription factor tfbs, transcription factor binding site eqtl, expression quantitative trait loci rsid, reference snp identifier

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DOI:
10.1016/j.csbj.2019.09.009

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