Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress.
Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress.
复制标题
DOI：
10.1371/journal.pone.0203266
复制
发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Singh A
中科院分区：
文献类型：
--
作者：
Sharma R;Singh G;Bhattacharya S;Singh A
多种环境胁迫对植物的生长和发育产生不利影响。植物在多重胁迫条件下会触发信号级联，并表现出对特定胁迫的独特反应以及对单个胁迫的共同反应。在这里，我们的目标是确定共同的和独特的遗传成分，在压力反应机制负责应力之间的串扰。尽管干旱和寒冷胁迫已被广泛研究，但关于它们的组合如何影响植物的信息却微不足道。为此，我们通过分析属于29个微阵列研究的390个微阵列样品，对拟南芥干旱和低温胁迫反应进行了荟萃分析和共表达网络比较。利用秩和积方法，我们分别观察到6120和7079个干旱和低温胁迫下的DEG（差异表达基因）。从统计学上看，28%（2890）的DEG被发现在两种应力（即;干旱和低温胁迫），其中大多数具有相似的表达模式。此外，基于基因本体的富集分析已经确定了共同的生物学过程和分子机制，如“光合作用”，“呼吸爆发”，“对干旱的反应”，“信号转导”，“代谢过程”，“对缺水的反应”，这些都受到寒冷和干旱胁迫的影响。43个转录因子家族被发现在两种胁迫条件下表达。Primycin、WRKY、NAC、MYB、AP 2/ERF和bZIP转录因子家族基因在所有基因集中高度富集，并被发现调控56%的干旱和低温胁迫下表达的共同基因。利用WGCNA（weighted gene co-expression network analysis）对基因共表达网络进行分析，结果表明，在干旱胁迫和低温胁迫下，分别有21个和16个基因模块具有高度相关性和特异表达谱。两种压力之间共享的基因模块的检测和分析揭示了四个共识基因模块的存在。
Multiple environmental stresses adversely affect plant growth and development. Plants under multiple stress condition trigger cascade of signals and show response unique to specific stress as well as shared responses, common to individual stresses. Here, we aim to identify common and unique genetic components during stress response mechanisms liable for cross-talk between stresses. Although drought and cold stress have been widely studied, insignificant information is available about how their combination affects plants. To that end, we performed meta-analysis and co-expression network comparison of drought and cold stress response in Arabidopsis thaliana by analyzing 390 microarray samples belonging to 29 microarray studies. We observed 6120 and 7079 DEGs (differentially expressed genes) under drought and cold stress respectively, using Rank Product methodology. Statistically, 28% (2890) DEGs were found to be common in both the stresses (i.e.; drought and cold stress) with most of them having similar expression pattern. Further, gene ontology-based enrichment analysis have identified shared biological processes and molecular mechanisms such as—‘photosynthesis’, ‘respiratory burst’, ‘response to hormone’, ‘signal transduction’, ‘metabolic process’, ‘response to water deprivation’, which were affected under cold and drought stress. Forty three transcription factor families were found to be expressed under both the stress conditions. Primarily, WRKY, NAC, MYB, AP2/ERF and bZIP transcription factor family genes were highly enriched in all genes sets and were found to regulate 56% of common genes expressed in drought and cold stress. Gene co-expression network analysis by WGCNA (weighted gene co-expression network analysis) revealed 21 and 16 highly inter-correlated gene modules with specific expression profiles under drought and cold stress respectively. Detection and analysis of gene modules shared between two stresses revealed the presence of four consensus gene modules.
登录
查看更多内容
WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
DOI：
10.3390/plants5030037
发表时间：
2016-09-06
期刊：
Plants (Basel, Switzerland)
影响因子：
--
作者：
Janack B;Sosoi P;Krupinska K;Humbeck K
通讯作者：
Humbeck K
影响因子：
4.3
作者：
Langfelder P;Luo R;Oldham MC;Horvath S
通讯作者：
Horvath S
影响因子：
2.1
作者：
MARANVILLE, JW;PAULSEN, GM
通讯作者：
PAULSEN, GM
agriGO：农业界的 GO 分析工具包
影响因子：
14.9
作者：
Du Z;Zhou X;Ling Y;Zhang Z;Su Z
通讯作者：
Su Z