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, Kouji 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, Sho 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 - 2007 Nov
Externally publishedYes

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

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and 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, Kouji; 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.

In: Bioinformatics, Vol. 23, No. 21, 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, Kouji ; 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. / 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, Kouji

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, Sho

AU - Ohara, Osamu

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