Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
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DOI：
10.1093/bioinformatics/btm430
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发表时间：
2007-11-01
期刊：
影响因子：
5.8
通讯作者：
Ohara, Osamu
中科院分区：
文献类型：
--
作者：
Hijikata, Atsushi;Kitamura, Hiroshi;Ohara, Osamu
动机：尽管大量的哺乳动物基因组数据确实是公开的，但在充分利用这些数据之前，生物学家仍有许多障碍需要克服。从基因组数据中获得生物学洞察力的挑战之一是无法使用单一的信息平台交叉参考转录和蛋白质组数据。为了解决这个问题，我们建立了一个开放的数据库，使我们能够交叉参考从免疫细胞获得的转录和蛋白质组数据。结果：该数据库名为RefDIC(免疫细胞参考基因组学数据库)，目前包含：(I)使用Affymetrix基因芯片技术获得的人和小鼠免疫细胞/组织的定量mRNA图谱；(Ii)通过双向凝胶电泳(2-DE)以及图像分析和质谱仪获得的小鼠免疫细胞的定量蛋白质图谱，以及(Iii)用于交叉参照免疫细胞的mRNA和蛋白质图谱的各种可视化工具。RefDIC是第一个开放获取的免疫基因组学数据库，是一个重要的信息共享平台，使免疫学中的基因组学方法成为可能。
Motivation: Although a huge amount of mammalian genomic data does become publicly available, there are still hurdles for biologists to overcome before such data can be fully exploited. One of the challenges for gaining biological insight from genomic data has been the inability to cross-reference transcriptomic and proteomic data using a single informational platform. To address this, we constructed an open-access database that enabled us to cross-reference transcriptomic and proteomic data obtained from immune cells.Results: The database, named RefDIC (Reference genomics Data-base of Immune Cells), currently contains: (i) quantitative mRNA profiles for human and mouse immune cells/tissues obtained using Affymetrix GeneChip technology; (ii) quantitative protein profiles for mouse immune cells obtained using two-dimensional gel electrophoresis (2-DE) followed by image analysis and mass spectrometry and (iii) various visualization tools to cross-reference the mRNA and protein profiles of immune cells. RefDIC is the first open-access database for immunogenomics and serves as an important information-sharing platform, enabling a focused genomic approach in immunology.