PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System.
10.1016/j.gpb.2018.08.002
- Author:
Huan QI
1
;
Zhenhong JIANG
2
;
Kang ZHANG
3
;
Shiping YANG
1
;
Fei HE
4
,
5
;
Ziding ZHANG
6
Author Information
1. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
2. Jiangxi Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China.
3. Department of Plant Pathology and the Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China.
4. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
5. Biology Department, Brookhaven National Lab, Upton, NY 11967, USA. Electronic address: feihe@ksu.edu.
6. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China. Electronic address: zidingzhang@cau.edu.cn.
- Publication Type:Journal Article
- Keywords:
Defense response;
Gene expression analysis;
PlaD;
Plant;
Transcriptomics database
- MeSH:
Arabidopsis;
genetics;
Databases, Genetic;
Gene Expression Profiling;
Gene Expression Regulation, Plant;
Gene Regulatory Networks;
Genes, Plant;
Host-Pathogen Interactions;
genetics;
Oryza;
genetics;
Plant Immunity;
genetics;
Plants;
genetics;
microbiology;
Transcriptome;
genetics;
Triticum;
genetics;
User-Computer Interface;
Zea mays;
genetics
- From:
Genomics, Proteomics & Bioinformatics
2018;16(4):283-293
- CountryChina
- Language:English
-
Abstract:
High-throughput transcriptomics technologies have been widely used to study plant transcriptional reprogramming during the process of plant defense responses, and a large quantity of gene expression data have been accumulated in public repositories. However, utilization of these data is often hampered by the lack of standard metadata annotation. In this study, we curated 2444 public pathogenesis-related gene expression samples from the model plant Arabidopsis and three major crops (maize, rice, and wheat). We organized the data into a user-friendly database termed as PlaD. Currently, PlaD contains three key features. First, it provides large-scale curated data related to plant defense responses, including gene expression and gene functional annotation data. Second, it provides the visualization of condition-specific expression profiles. Third, it allows users to search co-regulated genes under the infections of various pathogens. Using PlaD, we conducted a large-scale transcriptome analysis to explore the global landscape of gene expression in the curated data. We found that only a small fraction of genes were differentially expressed under multiple conditions, which might be explained by their tendency of having more network connections and shorter network distances in gene networks. Collectively, we hope that PlaD can serve as an important and comprehensive knowledgebase to the community of plant sciences, providing insightful clues to better understand the molecular mechanisms underlying plant immune responses. PlaD is freely available at http://systbio.cau.edu.cn/plad/index.php or http://zzdlab.com/plad/index.php.
