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 Oboki & 20 others Hiroshi 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, Shou Yamasaki, Osamu Ohara

    Research output: Contribution to journalArticle

    67 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 - Nov 1 2007

    Fingerprint

    Proteome
    Transcriptome
    Integrate
    Genomics
    Databases
    Proteins
    Cell
    Proteomics
    Messenger RNA
    Mouse
    Immunology
    Protein
    Electrophoresis
    Information Dissemination
    Image analysis
    Information Sharing
    Electrophoresis, Gel, Two-Dimensional
    Mass Spectrometry
    Mass spectrometry
    Allergy and Immunology

    All Science Journal Classification (ASJC) codes

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

    Cite this

    Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells. / 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, Shou; Ohara, Osamu.

    In: Bioinformatics, Vol. 23, No. 21, 01.11.2007, p. 2934-2941.

    Research output: Contribution to journalArticle

    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, Oboki, K, Ohno, H, Okamoto, M, Okayama, Y, O-Wang, J, Saito, H, Saito, T, Sakuma, M, Sato, K, Sato, K, Seino, KI, Setoguchi, R, Tamura, Y, Tanaka, M, Taniguchi, M, Taniuchi, I, Teng, A, Watanabe, T, Watarai, H, Yamasaki, S & Ohara, O 2007, 'Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells', Bioinformatics, vol. 23, no. 21, pp. 2934-2941. https://doi.org/10.1093/bioinformatics/btm430
    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, Shou ; Ohara, Osamu. / Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells. In: Bioinformatics. 2007 ; Vol. 23, No. 21. pp. 2934-2941.
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    AU - Hijikata, Atsushi

    AU - Kitamura, Hiroshi

    AU - Kimura, Yayoi

    AU - Yokoyama, Ryo

    AU - Aiba, Yuichi

    AU - Bao, Yanyuan

    AU - Fujita, Shigeharu

    AU - Hase, Koji

    AU - Hori, Shohei

    AU - Ishii, Yasuyuki

    AU - Kanagawa, Osami

    AU - Kawamoto, Hiroshi

    AU - Kawano, Kazuya

    AU - Koseki, Haruhiko

    AU - Kubo, Masato

    AU - Kurita-Miki, Ai

    AU - Kurosaki, Tomohiro

    AU - Masuda, Kyoko

    AU - Nakata, Mitsumasa

    AU - Oboki, Keisuke

    AU - Ohno, Hiroshi

    AU - Okamoto, Mariko

    AU - Okayama, Yoshimichi

    AU - O-Wang, Jiyang

    AU - Saito, Hirohisa

    AU - Saito, Takashi

    AU - Sakuma, Machie

    AU - Sato, Katsuaki

    AU - Sato, Kaori

    AU - Seino, Ken Ichiro

    AU - Setoguchi, Ruka

    AU - Tamura, Yuki

    AU - Tanaka, Masato

    AU - Taniguchi, Masaru

    AU - Taniuchi, Ichiro

    AU - Teng, Annabelle

    AU - Watanabe, Takeshi

    AU - Watarai, Hiroshi

    AU - Yamasaki, Shou

    AU - Ohara, Osamu

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    N2 - 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.

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