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croFGD: Catharanthus roseus Functional Genomics Database
Catharanthus roseus is a medicinal plant, which can produce monoterpene indole alkaloid (MIA) metabolites with biological activity and is rich in vinblastine and vincristine. With release of the scaffolded genome sequence of C. roseus, it is necessary to annotate gene functions on the whole-genome l...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438902/ https://www.ncbi.nlm.nih.gov/pubmed/30967897 http://dx.doi.org/10.3389/fgene.2019.00238 |
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author | She, Jiajie Yan, Hengyu Yang, Jiaotong Xu, Wenying Su, Zhen |
author_facet | She, Jiajie Yan, Hengyu Yang, Jiaotong Xu, Wenying Su, Zhen |
author_sort | She, Jiajie |
collection | PubMed |
description | Catharanthus roseus is a medicinal plant, which can produce monoterpene indole alkaloid (MIA) metabolites with biological activity and is rich in vinblastine and vincristine. With release of the scaffolded genome sequence of C. roseus, it is necessary to annotate gene functions on the whole-genome level. Recently, 53 RNA-seq datasets are available in public with different tissues (flower, root, leaf, seedling, and shoot) and different treatments (MeJA, PnWB infection and yeast elicitor). We used in-house data process pipeline with the combination of PCC and MR algorithms to construct a co-expression network exploring multi-dimensional gene expression (global, tissue preferential, and treat response) through multi-layered approaches. In the meanwhile, we added miRNA-target pairs, predicted PPI pairs into the network and provided several tools such as gene set enrichment analysis, functional module enrichment analysis, and motif analysis for functional prediction of the co-expression genes. Finally, we have constructed an online croFGD database (http://bioinformatics.cau.edu.cn/croFGD/). We hope croFGD can help the communities to study the C. roseus functional genomics and make novel discoveries about key genes involved in some important biological processes. |
format | Online Article Text |
id | pubmed-6438902 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-64389022019-04-09 croFGD: Catharanthus roseus Functional Genomics Database She, Jiajie Yan, Hengyu Yang, Jiaotong Xu, Wenying Su, Zhen Front Genet Genetics Catharanthus roseus is a medicinal plant, which can produce monoterpene indole alkaloid (MIA) metabolites with biological activity and is rich in vinblastine and vincristine. With release of the scaffolded genome sequence of C. roseus, it is necessary to annotate gene functions on the whole-genome level. Recently, 53 RNA-seq datasets are available in public with different tissues (flower, root, leaf, seedling, and shoot) and different treatments (MeJA, PnWB infection and yeast elicitor). We used in-house data process pipeline with the combination of PCC and MR algorithms to construct a co-expression network exploring multi-dimensional gene expression (global, tissue preferential, and treat response) through multi-layered approaches. In the meanwhile, we added miRNA-target pairs, predicted PPI pairs into the network and provided several tools such as gene set enrichment analysis, functional module enrichment analysis, and motif analysis for functional prediction of the co-expression genes. Finally, we have constructed an online croFGD database (http://bioinformatics.cau.edu.cn/croFGD/). We hope croFGD can help the communities to study the C. roseus functional genomics and make novel discoveries about key genes involved in some important biological processes. Frontiers Media S.A. 2019-03-22 /pmc/articles/PMC6438902/ /pubmed/30967897 http://dx.doi.org/10.3389/fgene.2019.00238 Text en Copyright © 2019 She, Yan, Yang, Xu and Su. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics She, Jiajie Yan, Hengyu Yang, Jiaotong Xu, Wenying Su, Zhen croFGD: Catharanthus roseus Functional Genomics Database |
title | croFGD: Catharanthus roseus Functional Genomics Database |
title_full | croFGD: Catharanthus roseus Functional Genomics Database |
title_fullStr | croFGD: Catharanthus roseus Functional Genomics Database |
title_full_unstemmed | croFGD: Catharanthus roseus Functional Genomics Database |
title_short | croFGD: Catharanthus roseus Functional Genomics Database |
title_sort | crofgd: catharanthus roseus functional genomics database |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438902/ https://www.ncbi.nlm.nih.gov/pubmed/30967897 http://dx.doi.org/10.3389/fgene.2019.00238 |
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