agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species.
Selina KleesFelix HeinrichArmin Otto SchmittMehmet GültasPublished in: Biology (2021)
Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters. Today, it is well known that single nucleotide polymorphisms (SNPs) in TFBSs can dramatically affect the level of gene expression, since they can cause a change in the binding affinity of TFs. Such SNPs, referred to as regulatory SNPs (rSNPs), have gained attention in the life sciences due to their causality for specific traits or diseases. In this study, we present agReg-SNPdb, a database comprising rSNP data of seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog. To identify the rSNPs, we constructed a bioinformatics pipeline and identified a total of 10,623,512 rSNPs, which are located within TFBSs and affect the binding affinity of putative TFs. Altogether, we implemented the first systematic analysis of SNPs in promoter regions and their impact on the binding affinity of TFs for livestock and made it usable via a web interface.
Keyphrases
- transcription factor
- genome wide
- dna binding
- dna methylation
- gene expression
- genome wide association
- risk assessment
- adverse drug
- heavy metals
- genome wide identification
- binding protein
- wastewater treatment
- oxidative stress
- working memory
- electronic health record
- single molecule
- human health
- emergency department
- circulating tumor
- big data
- drug induced