Nakamura Yukino, Kudo Toru, Terashima Shin, Saito Misa, Nambara Eiji, Yano Kentaro
Bioinformatics Laboratory, School of Agriculture, Meiji University, Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
Department of Cell & Systems Biology, University of Toronto, Willcocks Street, Toronto, Ontario, Canada.
Plant Cell Physiol. 2017 Jan 1;58(1):e3. doi: 10.1093/pcp/pcw199.
For proper control of biological activity, some key genes are highly expressed in a particular spatiotemporal domain. Mining of such spatiotemporally expressed genes using large-scale gene expression data derived from a broad range of experimental sources facilitates our understanding of genome-scale functional gene networks. However, comprehensive information on spatiotemporally expressed genes is lacking in plants. To collect such information, we devised a new index, Δdmax, which is the maximum difference in relative gene expression levels between sample runs which are neighboring when sorted by the levels. Employing this index, we comprehensively evaluated transcripts using large-scale RNA sequencing (RNA-Seq) data stored in the Sequence Read Archive for eight plant species: Arabidopsis thaliana (Arabidopsis), Solanum lycopersicum (tomato), Solanum tuberosum (potato), Oryza sativa (rice), Sorghum bicolor (sorghum), Vitis vinifera (grape), Medicago truncatula (Medicago), and Glycine max (soybean). Based on the frequency distribution of the Δdmax values, approximately 70,000 transcripts showing 0.3 or larger Δdmax values were extracted for the eight species. Information on these genes including the Δdmax values, functional annotations, conservation among species, and experimental conditions where the genes show high expression levels is provided in a new database, CATchUP (http://plantomics.mind.meiji.ac.jp/CATchUP). The CATchUP database assists in identifying genes specifically expressed under particular conditions with powerful search functions and an intuitive graphical user interface.
为了对生物活性进行适当控制，一些关键基因在特定的时空域中高度表达。利用来自广泛实验来源的大规模基因表达数据挖掘此类时空表达基因，有助于我们理解基因组规模的功能基因网络。然而，植物中缺乏关于时空表达基因的全面信息。为了收集此类信息，我们设计了一个新的指标Δdmax，它是按水平排序时相邻样本运行之间相对基因表达水平的最大差异。利用这个指标，我们使用存储在序列读取存档中的大规模RNA测序（RNA-Seq）数据，对八种植物进行了转录本的综合评估：拟南芥、番茄、马铃薯、水稻、高粱、葡萄、蒺藜苜蓿和大豆。根据Δdmax值的频率分布，从这八个物种中提取了大约70000个Δdmax值为0.3或更大的转录本。一个新的数据库CATchUP（http://plantomics.mind.meiji.ac.jp/CATchUP）提供了关于这些基因的信息，包括Δdmax值、功能注释、物种间的保守性以及基因显示高表达水平的实验条件。CATchUP数据库通过强大的搜索功能和直观的图形用户界面，有助于识别在特定条件下特异性表达的基因。
