agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species
Single nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs...
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MDPI AG
2022-04-01
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| Online Access: | https://www.mdpi.com/2079-7737/11/5/684 |
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| author | Selina Klees Felix Heinrich Armin Otto Schmitt Mehmet Gültas |
| author_facet | Selina Klees Felix Heinrich Armin Otto Schmitt Mehmet Gültas |
| author_sort | Selina Klees |
| collection | DOAJ |
| description | Single nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs can reveal the biologically causative variant and decipher the regulatory mechanisms behind a phenotype. In our previous work, we presented agReg-SNPdb, a database of regulatory SNPs for agriculturally important animal species. To complement this previous work, in this study we present the extension agReg-SNPdb-Plants storing rSNPs and their predicted effects on TF-binding for 13 agriculturally important plant species and subspecies (<i>Brassica napus</i>, <i>Helianthus annuus</i>, <i>Hordeum vulgare</i>, <i>Oryza glaberrima</i>, <i>Oryza glumipatula</i>, <i>Oryza sativa</i> Indica, <i>Oryza sativa</i> Japonica, <i>Solanum lycopersicum</i>, <i>Sorghum bicolor</i>, <i>Triticum aestivum</i>, <i>Triticum turgidum</i>, <i>Vitis vinifera</i>, and <i>Zea mays</i>). agReg-SNPdb-Plants can be queried via a web interface that allows users to search for SNP IDs, chromosomal regions, or genes. For a comprehensive interpretation of GWAS results or larger SNP-sets, it is possible to download the whole list of SNPs and their impact on transcription factor binding sites (TFBSs) from the website chromosome-wise. |
| first_indexed | 2024-03-10T03:19:10Z |
| format | Article |
| id | doaj.art-1be388ed79bc42658f1614b73e10e969 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-10T03:19:10Z |
| publishDate | 2022-04-01 |
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| record_format | Article |
| series | Biology |
| spelling | doaj.art-1be388ed79bc42658f1614b73e10e9692023-11-23T10:06:59ZengMDPI AGBiology2079-77372022-04-0111568410.3390/biology11050684agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant SpeciesSelina Klees0Felix Heinrich1Armin Otto Schmitt2Mehmet Gültas3Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, GermanyBreeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, GermanyBreeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, GermanyCenter for Integrated Breeding Research (CiBreed), Carl-Sprengel-Weg 1, Georg-August University, 37075 Göttingen, GermanySingle nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs can reveal the biologically causative variant and decipher the regulatory mechanisms behind a phenotype. In our previous work, we presented agReg-SNPdb, a database of regulatory SNPs for agriculturally important animal species. To complement this previous work, in this study we present the extension agReg-SNPdb-Plants storing rSNPs and their predicted effects on TF-binding for 13 agriculturally important plant species and subspecies (<i>Brassica napus</i>, <i>Helianthus annuus</i>, <i>Hordeum vulgare</i>, <i>Oryza glaberrima</i>, <i>Oryza glumipatula</i>, <i>Oryza sativa</i> Indica, <i>Oryza sativa</i> Japonica, <i>Solanum lycopersicum</i>, <i>Sorghum bicolor</i>, <i>Triticum aestivum</i>, <i>Triticum turgidum</i>, <i>Vitis vinifera</i>, and <i>Zea mays</i>). agReg-SNPdb-Plants can be queried via a web interface that allows users to search for SNP IDs, chromosomal regions, or genes. For a comprehensive interpretation of GWAS results or larger SNP-sets, it is possible to download the whole list of SNPs and their impact on transcription factor binding sites (TFBSs) from the website chromosome-wise.https://www.mdpi.com/2079-7737/11/5/684regulatory SNPtranscription factortranscription factor binding sitegene regulationGWASdatabase |
| spellingShingle | Selina Klees Felix Heinrich Armin Otto Schmitt Mehmet Gültas agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species Biology regulatory SNP transcription factor transcription factor binding site gene regulation GWAS database |
| title | agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species |
| title_full | agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species |
| title_fullStr | agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species |
| title_full_unstemmed | agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species |
| title_short | agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species |
| title_sort | agreg snpdb plants a database of regulatory snps for agricultural plant species |
| topic | regulatory SNP transcription factor transcription factor binding site gene regulation GWAS database |
| url | https://www.mdpi.com/2079-7737/11/5/684 |
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