利用荟萃分析挖掘拟南芥低温胁迫响应基因

Meta-analysis Identify Candidate Genes for Cold Stress Response in Arabidopsis

低温胁迫是目前威胁全球作物产量的重要非生物胁迫因子之一。有效地克服不同微阵列芯片测序分析间的不一致性,科学地预测拟南芥(Arabidopsis thaliana)低温胁迫响应基因和其关联的生物学过程是挖掘拟南芥响应冷胁迫的分子机制和辅助研发抗冷作物的有效手段之一。本研究首先利用关键词在PubMed数据库、GEO(Gene Expression Omnibus)数据库和Array Express数据库分别筛选出1 166、298个和695个测序实验,并通过精细筛选得到8组含低温胁迫处理样本和对照样本的表达谱测序实验。利用Network Analyst网站的批量效应矫正分析(batch effect correction)和有效样本数目(Effect size analysis)整合方法来降低8组表达数据实验间的不一致性并进行荟萃整合分析,进一步筛选出1 553个上调基因和4 327个下调基因。基于功能富集分析结果和转录因子(transcriptional factors,TFs)、蛋白激酶(protein kinases,PKs)和植物内源激素途径成员的差异表达式样,预测植物激素关联的胁迫感受途径、离子和激酶关联的信号通路及转录调控过程是拟南芥响应寒冷胁迫潜在的关键途径。

Cold stress is one of the major environmental limitations to agricultural productivity throughout the world. Overcoming the defects of microarray sequencing analyses caused by heterogeneity in individual studies and prediction of cold stress response candidate genes and pathways in Arabidopsis thaliana are requisite for cold tolerant crop-plant design and mining potential salt responses mechanisms. A literature searching strategy was used to identify salt stress response expression profiling studies in Arabidopsis from the PubMed database, the Gene Expression Omnibus （GEO） database, and the ArrayExpress database. Eight studies were filtered from the I 166, 298 and 695 identified studies. The batch effect correction and the effect size analysis based on the NetworkAnalyst web tool were combined to integrate 8 microarray datasets, and 1 553 up-regulated and 4 327 down-regulated were identified with in low temperature treated samples. From the functional enrichment analyses results and the differently spatio-temporal expression patterns of transcriptional factors （TFs）, protein kinases （PKs） and several plant hormone-related genes, plant hormone related stress signal construction pathways, ion and protein kinases related signaling pathways and transcriptional regulation were predicted to participate in regulating cold stress response in Arabidopsis.