Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scans
In the post-GWAS (Genome-Wide Association Scan) era, the interpretation of GWAS results is crucial to screen for highly relevant phenotype-genotype association pairs. Based on the single genotype-phenotype association test and a pathway enrichment analysis, we propose a Metabolite-pathway-based Phen...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-11-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.01027/full |
| _version_ | 1818965199535734784 |
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| author | Yaping eLu Yemao eLiu Xiaohui eNiu Qingyong eYang Xuehai eHu Hong-Yu eZhang Jingbo eXia |
| author_facet | Yaping eLu Yemao eLiu Xiaohui eNiu Qingyong eYang Xuehai eHu Hong-Yu eZhang Jingbo eXia |
| author_sort | Yaping eLu |
| collection | DOAJ |
| description | In the post-GWAS (Genome-Wide Association Scan) era, the interpretation of GWAS results is crucial to screen for highly relevant phenotype-genotype association pairs. Based on the single genotype-phenotype association test and a pathway enrichment analysis, we propose a Metabolite-pathway-based Phenome-Wide Association Scan (M-PheWAS) to analyze the key metabolite-SNP pairs in rice and determine the regulatory relationship by assessing similarities in the changes of enzymes and downstream products in a pathway. Two SNPs, sf0315305925 and sf0315308337, were selected using this approach, and their molecular function and regulatory relationship with Enzyme EC:5.5.1.6 and with flavonoids, a significant downstream regulatory metabolite product, were demonstrated. Moreover, a total of 105 crucial SNPs were screened using M-PheWAS, which may be important for metabolite associations. |
| first_indexed | 2024-12-20T13:13:13Z |
| format | Article |
| id | doaj.art-26a9a34f8f654238b81a13c40ce85371 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-20T13:13:13Z |
| publishDate | 2015-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-26a9a34f8f654238b81a13c40ce853712022-12-21T19:39:37ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2015-11-01610.3389/fpls.2015.01027165658Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scansYaping eLu0Yemao eLiu1Xiaohui eNiu2Qingyong eYang3Xuehai eHu4Hong-Yu eZhang5Jingbo eXia6College of informatics, Huazhong Agricultural UnivCollege of informatics, Huazhong Agricultural UnivCollege of informatics, Huazhong Agricultural UnivCollege of informatics, Huazhong Agricultural UnivCollege of informatics, Huazhong Agricultural UnivCollege of informatics, Huazhong Agricultural UnivCollege of informatics, Huazhong Agricultural UnivIn the post-GWAS (Genome-Wide Association Scan) era, the interpretation of GWAS results is crucial to screen for highly relevant phenotype-genotype association pairs. Based on the single genotype-phenotype association test and a pathway enrichment analysis, we propose a Metabolite-pathway-based Phenome-Wide Association Scan (M-PheWAS) to analyze the key metabolite-SNP pairs in rice and determine the regulatory relationship by assessing similarities in the changes of enzymes and downstream products in a pathway. Two SNPs, sf0315305925 and sf0315308337, were selected using this approach, and their molecular function and regulatory relationship with Enzyme EC:5.5.1.6 and with flavonoids, a significant downstream regulatory metabolite product, were demonstrated. Moreover, a total of 105 crucial SNPs were screened using M-PheWAS, which may be important for metabolite associations.http://journal.frontiersin.org/Journal/10.3389/fpls.2015.01027/fullreplicationmetaboliteWilcoxon rank-sum testAssociation scanupper tier metabolite pathway |
| spellingShingle | Yaping eLu Yemao eLiu Xiaohui eNiu Qingyong eYang Xuehai eHu Hong-Yu eZhang Jingbo eXia Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scans Frontiers in Plant Science replication metabolite Wilcoxon rank-sum test Association scan upper tier metabolite pathway |
| title | Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scans |
| title_full | Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scans |
| title_fullStr | Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scans |
| title_full_unstemmed | Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scans |
| title_short | Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scans |
| title_sort | systems genetic validation of the snp metabolite association in rice via metabolite pathway based phenome wide association scans |
| topic | replication metabolite Wilcoxon rank-sum test Association scan upper tier metabolite pathway |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.01027/full |
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