Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells

Atsushi Hijikata, Hiroshi Kitamura, Yayoi Kimura, Ryo Yokoyama, Yuichi Aiba, Yanyuan Bao, Shigeharu Fujita, Koji Hase, Shohei Hori, Yasuyuki Ishii, Osami Kanagawa, Hiroshi Kawamoto, Kazuya Kawano, Haruhiko Koseki, Masato Kubo, Ai Kurita-Miki, Tomohiro Kurosaki, Kyoko Masuda, Mitsumasa Nakata, Keisuke ObokiHiroshi Ohno, Mariko Okamoto, Yoshimichi Okayama, Jiyang O-Wang, Hirohisa Saito, Takashi Saito, Machie Sakuma, Katsuaki Sato, Kaori Sato, Ken Ichiro Seino, Ruka Setoguchi, Yuki Tamura, Masato Tanaka, Masaru Taniguchi, Ichiro Taniuchi, Annabelle Teng, Takeshi Watanabe, Hiroshi Watarai, Sho Yamasaki, Osamu Ohara

Research output: Contribution to journalArticle

69 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)2934-2941
Number of pages8
JournalBioinformatics
Volume23
Issue number21
DOIs
Publication statusPublished - 2007 Nov 1

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ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Hijikata, A., Kitamura, H., Kimura, Y., Yokoyama, R., Aiba, Y., Bao, Y., Fujita, S., Hase, K., Hori, S., Ishii, Y., Kanagawa, O., Kawamoto, H., Kawano, K., Koseki, H., Kubo, M., Kurita-Miki, A., Kurosaki, T., Masuda, K., Nakata, M., ... Ohara, O. (2007). Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells. Bioinformatics, 23(21), 2934-2941. https://doi.org/10.1093/bioinformatics/btm430