构建一个开放获取的数据库，该数据库整合了免疫细胞转录组和蛋白质组的交叉参考信息。
Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells.
作者信息
Hijikata Atsushi, Kitamura Hiroshi, Kimura Yayoi, Yokoyama Ryo, Aiba Yuichi, Bao Yanyuan, Fujita Shigeharu, Hase Koji, Hori Shohei, Ishii Yasuyuki, Kanagawa Osami, Kawamoto Hiroshi, Kawano Kazuya, Koseki Haruhiko, Kubo Masato, Kurita-Miki Ai, Kurosaki Tomohiro, Masuda Kyoko, Nakata Mitsumasa, Oboki Keisuke, Ohno Hiroshi, Okamoto Mariko, Okayama Yoshimichi, O-Wang Jiyang, Saito Hirohisa, Saito Takashi, Sakuma Machie, Sato Katsuaki, Sato Kaori, Seino Ken-ichiro, Setoguchi Ruka, Tamura Yuki, Tanaka Masato, Taniguchi Masaru, Taniuchi Ichiro, Teng Annabelle, Watanabe Takeshi, Watarai Hiroshi, Yamasaki Sho, Ohara Osamu
机构信息
RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
出版信息
Bioinformatics. 2007 Nov 1;23(21):2934-41. doi: 10.1093/bioinformatics/btm430. Epub 2007 Sep 24.
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 Database 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.
AVAILABILITY
All raw data and information can be accessed from http://refdic.rcai.riken.jp/. The microarray data is also available at http://cibex.nig.ac.jp/ under CIBEX accession no. CBX19, and http://www.ebi.ac.uk/pride/ under PRIDE accession numbers 2354-2378 and 2414.
动机
尽管大量哺乳动物基因组数据已公开可用，但在这些数据能够得到充分利用之前，生物学家仍需克服一些障碍。从基因组数据中获取生物学见解面临的挑战之一是无法使用单一信息平台对转录组数据和蛋白质组数据进行交叉引用。为了解决这个问题，我们构建了一个开放获取的数据库，使我们能够对从免疫细胞获得的转录组数据和蛋白质组数据进行交叉引用。
结果
该数据库名为RefDIC（免疫细胞参考基因组数据库），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谱；（ii）使用二维凝胶电泳（2-DE），随后进行图像分析和质谱分析获得的小鼠免疫细胞的定量蛋白质谱，以及（iii）各种可视化工具，用于交叉引用免疫细胞的mRNA和蛋白质谱。RefDIC是第一个用于免疫基因组学的开放获取数据库，是一个重要的信息共享平台，有助于在免疫学中采用聚焦的基因组方法。
可用性
所有原始数据和信息可从http://refdic.rcai.riken.jp/获取。微阵列数据也可在http://cibex.nig.ac.jp/下以CIBEX登录号CBX19获取，以及在http://www.ebi.ac.uk/pride/下以PRIDE登录号2354 - 2378和2414获取。
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