GelFAP: Gene Functional Analysis Platform for Gastrodia elata
Gastrodia elata, also named Tianma, is a valuable traditional Chinese herbal medicine. It has numerous important pharmacological roles such as in sedation and lowering blood pressure and as anticonvulsant and anti-aging, and it also has effects on the immune and cardiovascular systems. The whole gen...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-10-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2020.563237/full |
| _version_ | 1831647902530797568 |
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| author | Jiaotong Yang Qiaoqiao Xiao Jiao Xu Lingling Da Lanping Guo Luqi Huang Yue Liu Wenying Xu Zhen Su Shiping Yang Qi Pan Weike Jiang Tao Zhou |
| author_facet | Jiaotong Yang Qiaoqiao Xiao Jiao Xu Lingling Da Lanping Guo Luqi Huang Yue Liu Wenying Xu Zhen Su Shiping Yang Qi Pan Weike Jiang Tao Zhou |
| author_sort | Jiaotong Yang |
| collection | DOAJ |
| description | Gastrodia elata, also named Tianma, is a valuable traditional Chinese herbal medicine. It has numerous important pharmacological roles such as in sedation and lowering blood pressure and as anticonvulsant and anti-aging, and it also has effects on the immune and cardiovascular systems. The whole genome sequencing of G. elata has been completed in recent years, which provides a strong support for the construction of the G. elata gene functional analysis platform. Therefore, in our research, we collected and processed 39 transcriptome data of G. elata and constructed the G. elata gene co-expression networks, then we identified functional modules by the weighted correlation network analysis (WGCNA) package. Furthermore, gene families of G. elata were identified by tools including HMMER, iTAK, PfamScan, and InParanoid. Finally, we constructed a gene functional analysis platform for G. elata1. In our platform, we introduced functional analysis tools such as BLAST, gene set enrichment analysis (GSEA), and cis-elements (motif) enrichment analysis tool. In addition, we analyzed the co-expression relationship of genes which might participate in the biosynthesis of gastrodin and predicted 19 mannose-binding lectin antifungal proteins of G. elata. We also introduced the usage of the G. elata gene function analysis platform (GelFAP) by analyzing CYP51G1 and GFAP4 genes. Our platform GelFAP may help researchers to explore the gene function of G. elata and make novel discoveries about key genes involved in the biological processes of gastrodin. |
| first_indexed | 2024-12-19T14:21:50Z |
| format | Article |
| id | doaj.art-65c4f84be6474f5fab166e639a670f27 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-19T14:21:50Z |
| publishDate | 2020-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-65c4f84be6474f5fab166e639a670f272022-12-21T20:17:45ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2020-10-011110.3389/fpls.2020.563237563237GelFAP: Gene Functional Analysis Platform for Gastrodia elataJiaotong Yang0Qiaoqiao Xiao1Jiao Xu2Lingling Da3Lanping Guo4Luqi Huang5Yue Liu6Wenying Xu7Zhen Su8Shiping Yang9Qi Pan10Weike Jiang11Tao Zhou12Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, ChinaSource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, ChinaSource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, ChinaCollege of Biological Sciences, China Agricultural University, Beijing, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, ChinaCollege of Horticulture, Qingdao Agricultural University, Qingdao, ChinaCollege of Biological Sciences, China Agricultural University, Beijing, ChinaCollege of Biological Sciences, China Agricultural University, Beijing, ChinaCollege of Biological Sciences, China Agricultural University, Beijing, ChinaSource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, ChinaSource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, ChinaSource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, ChinaGastrodia elata, also named Tianma, is a valuable traditional Chinese herbal medicine. It has numerous important pharmacological roles such as in sedation and lowering blood pressure and as anticonvulsant and anti-aging, and it also has effects on the immune and cardiovascular systems. The whole genome sequencing of G. elata has been completed in recent years, which provides a strong support for the construction of the G. elata gene functional analysis platform. Therefore, in our research, we collected and processed 39 transcriptome data of G. elata and constructed the G. elata gene co-expression networks, then we identified functional modules by the weighted correlation network analysis (WGCNA) package. Furthermore, gene families of G. elata were identified by tools including HMMER, iTAK, PfamScan, and InParanoid. Finally, we constructed a gene functional analysis platform for G. elata1. In our platform, we introduced functional analysis tools such as BLAST, gene set enrichment analysis (GSEA), and cis-elements (motif) enrichment analysis tool. In addition, we analyzed the co-expression relationship of genes which might participate in the biosynthesis of gastrodin and predicted 19 mannose-binding lectin antifungal proteins of G. elata. We also introduced the usage of the G. elata gene function analysis platform (GelFAP) by analyzing CYP51G1 and GFAP4 genes. Our platform GelFAP may help researchers to explore the gene function of G. elata and make novel discoveries about key genes involved in the biological processes of gastrodin.https://www.frontiersin.org/articles/10.3389/fpls.2020.563237/fullGastrodia elataco-expression networkfunctional modulegene functional analysis platformfunctional enrichment analysis |
| spellingShingle | Jiaotong Yang Qiaoqiao Xiao Jiao Xu Lingling Da Lanping Guo Luqi Huang Yue Liu Wenying Xu Zhen Su Shiping Yang Qi Pan Weike Jiang Tao Zhou GelFAP: Gene Functional Analysis Platform for Gastrodia elata Frontiers in Plant Science Gastrodia elata co-expression network functional module gene functional analysis platform functional enrichment analysis |
| title | GelFAP: Gene Functional Analysis Platform for Gastrodia elata |
| title_full | GelFAP: Gene Functional Analysis Platform for Gastrodia elata |
| title_fullStr | GelFAP: Gene Functional Analysis Platform for Gastrodia elata |
| title_full_unstemmed | GelFAP: Gene Functional Analysis Platform for Gastrodia elata |
| title_short | GelFAP: Gene Functional Analysis Platform for Gastrodia elata |
| title_sort | gelfap gene functional analysis platform for gastrodia elata |
| topic | Gastrodia elata co-expression network functional module gene functional analysis platform functional enrichment analysis |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2020.563237/full |
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