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In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis
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| Zeitschriftentitel: | Journal of Cellular Physiology |
|---|---|
| Personen und Körperschaften: | , , , , |
| In: | Journal of Cellular Physiology, 235, 2020, 2, S. 900-908 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Wiley
|
| Schlagwörter: |
| author_facet |
Lin, Weimin Xu, Hao Wu, Yunshu Wang, Jun Yuan, Quan Lin, Weimin Xu, Hao Wu, Yunshu Wang, Jun Yuan, Quan |
|---|---|
| author |
Lin, Weimin Xu, Hao Wu, Yunshu Wang, Jun Yuan, Quan |
| spellingShingle |
Lin, Weimin Xu, Hao Wu, Yunshu Wang, Jun Yuan, Quan Journal of Cellular Physiology In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis Cell Biology Clinical Biochemistry Physiology |
| author_sort |
lin, weimin |
| spelling |
Lin, Weimin Xu, Hao Wu, Yunshu Wang, Jun Yuan, Quan 0021-9541 1097-4652 Wiley Cell Biology Clinical Biochemistry Physiology http://dx.doi.org/10.1002/jcp.29005 <jats:title>Abstract</jats:title><jats:p>Genetic variation is considered to affect the <jats:italic>N</jats:italic><jats:sup>6</jats:sup>‐methyladenosine (m6A) RNA transcript modification, which is the most prevalent posttranscriptional messenger RNA modification. This study aimed to identify m6A‐associated single‐nucleotide polymorphisms (m6A‐SNPs) that may affect m6A methylation from numerous periodontitis (PD) SNPs. We identified an abundance of m6A‐SNPs by analyzing raw data of published PD genome‐wide association studies and m6A‐SNPs list from the m6AVar database. Other evidence was found in public databases for expression quantitative trait loci (eQTL) and differential gene expression analysis. Accordingly, 1938 m6A‐SNPs were identified, 104 of which appeared to be associated with PD (<jats:italic>p</jats:italic> < .05) while 65 showed eQTL signals. Lastly, the leading SNP rs2723183 (<jats:italic>p</jats:italic> = 3.93E−07) was predicted to regulate local gene <jats:italic>IL‐37</jats:italic> expression in PD (<jats:italic>p</jats:italic> = 2.64E−05; in GSE10334) and change regulatory motif RXRA. In summary, dozens of PD‐associated m6A‐SNPs were identified and their possible functions were demonstrated in this study.</jats:p> In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis Journal of Cellular Physiology |
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10.1002/jcp.29005 |
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Journal of Cellular Physiology |
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| title |
In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_unstemmed |
In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_full |
In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_fullStr |
In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_full_unstemmed |
In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_short |
In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_sort |
in silico genome‐wide identification of m6a‐associated snps as potential functional variants for periodontitis |
| topic |
Cell Biology Clinical Biochemistry Physiology |
| url |
http://dx.doi.org/10.1002/jcp.29005 |
| publishDate |
2020 |
| physical |
900-908 |
| description |
<jats:title>Abstract</jats:title><jats:p>Genetic variation is considered to affect the <jats:italic>N</jats:italic><jats:sup>6</jats:sup>‐methyladenosine (m6A) RNA transcript modification, which is the most prevalent posttranscriptional messenger RNA modification. This study aimed to identify m6A‐associated single‐nucleotide polymorphisms (m6A‐SNPs) that may affect m6A methylation from numerous periodontitis (PD) SNPs. We identified an abundance of m6A‐SNPs by analyzing raw data of published PD genome‐wide association studies and m6A‐SNPs list from the m6AVar database. Other evidence was found in public databases for expression quantitative trait loci (eQTL) and differential gene expression analysis. Accordingly, 1938 m6A‐SNPs were identified, 104 of which appeared to be associated with PD (<jats:italic>p</jats:italic> < .05) while 65 showed eQTL signals. Lastly, the leading SNP rs2723183 (<jats:italic>p</jats:italic> = 3.93E−07) was predicted to regulate local gene <jats:italic>IL‐37</jats:italic> expression in PD (<jats:italic>p</jats:italic> = 2.64E−05; in GSE10334) and change regulatory motif RXRA. In summary, dozens of PD‐associated m6A‐SNPs were identified and their possible functions were demonstrated in this study.</jats:p> |
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| author | Lin, Weimin, Xu, Hao, Wu, Yunshu, Wang, Jun, Yuan, Quan |
| author_facet | Lin, Weimin, Xu, Hao, Wu, Yunshu, Wang, Jun, Yuan, Quan, Lin, Weimin, Xu, Hao, Wu, Yunshu, Wang, Jun, Yuan, Quan |
| author_sort | lin, weimin |
| container_issue | 2 |
| container_start_page | 900 |
| container_title | Journal of Cellular Physiology |
| container_volume | 235 |
| description | <jats:title>Abstract</jats:title><jats:p>Genetic variation is considered to affect the <jats:italic>N</jats:italic><jats:sup>6</jats:sup>‐methyladenosine (m6A) RNA transcript modification, which is the most prevalent posttranscriptional messenger RNA modification. This study aimed to identify m6A‐associated single‐nucleotide polymorphisms (m6A‐SNPs) that may affect m6A methylation from numerous periodontitis (PD) SNPs. We identified an abundance of m6A‐SNPs by analyzing raw data of published PD genome‐wide association studies and m6A‐SNPs list from the m6AVar database. Other evidence was found in public databases for expression quantitative trait loci (eQTL) and differential gene expression analysis. Accordingly, 1938 m6A‐SNPs were identified, 104 of which appeared to be associated with PD (<jats:italic>p</jats:italic> < .05) while 65 showed eQTL signals. Lastly, the leading SNP rs2723183 (<jats:italic>p</jats:italic> = 3.93E−07) was predicted to regulate local gene <jats:italic>IL‐37</jats:italic> expression in PD (<jats:italic>p</jats:italic> = 2.64E−05; in GSE10334) and change regulatory motif RXRA. In summary, dozens of PD‐associated m6A‐SNPs were identified and their possible functions were demonstrated in this study.</jats:p> |
| doi_str_mv | 10.1002/jcp.29005 |
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| spelling | Lin, Weimin Xu, Hao Wu, Yunshu Wang, Jun Yuan, Quan 0021-9541 1097-4652 Wiley Cell Biology Clinical Biochemistry Physiology http://dx.doi.org/10.1002/jcp.29005 <jats:title>Abstract</jats:title><jats:p>Genetic variation is considered to affect the <jats:italic>N</jats:italic><jats:sup>6</jats:sup>‐methyladenosine (m6A) RNA transcript modification, which is the most prevalent posttranscriptional messenger RNA modification. This study aimed to identify m6A‐associated single‐nucleotide polymorphisms (m6A‐SNPs) that may affect m6A methylation from numerous periodontitis (PD) SNPs. We identified an abundance of m6A‐SNPs by analyzing raw data of published PD genome‐wide association studies and m6A‐SNPs list from the m6AVar database. Other evidence was found in public databases for expression quantitative trait loci (eQTL) and differential gene expression analysis. Accordingly, 1938 m6A‐SNPs were identified, 104 of which appeared to be associated with PD (<jats:italic>p</jats:italic> < .05) while 65 showed eQTL signals. Lastly, the leading SNP rs2723183 (<jats:italic>p</jats:italic> = 3.93E−07) was predicted to regulate local gene <jats:italic>IL‐37</jats:italic> expression in PD (<jats:italic>p</jats:italic> = 2.64E−05; in GSE10334) and change regulatory motif RXRA. In summary, dozens of PD‐associated m6A‐SNPs were identified and their possible functions were demonstrated in this study.</jats:p> In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis Journal of Cellular Physiology |
| spellingShingle | Lin, Weimin, Xu, Hao, Wu, Yunshu, Wang, Jun, Yuan, Quan, Journal of Cellular Physiology, In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis, Cell Biology, Clinical Biochemistry, Physiology |
| title | In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_full | In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_fullStr | In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_full_unstemmed | In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_short | In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| title_sort | in silico genome‐wide identification of m6a‐associated snps as potential functional variants for periodontitis |
| title_unstemmed | In silico genome‐wide identification of m6A‐associated SNPs as potential functional variants for periodontitis |
| topic | Cell Biology, Clinical Biochemistry, Physiology |
| url | http://dx.doi.org/10.1002/jcp.29005 |