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

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 tr... Full description

Journal Title: Bioinformatics 2007, Vol. 23(21), pp.2934-2941
Main Author: Hijikata, Atsushi
Other Authors: 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
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ID: ISSN: 1367-4803 ; E-ISSN: 1460-2059 ; DOI: 10.1093/bioinformatics/btm430
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recordid: oxford10.1093/bioinformatics/btm430
title: Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
format: Article
creator:
  • 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
subjects:
  • Biology
ispartof: Bioinformatics, 2007, Vol. 23(21), pp.2934-2941
description: 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. The database, named RefDIC (erence genomics atabase of mmune ells), 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. All raw data and information can be accessed from . The microarray data is also available at under CIBEX accession no. CBX19, and under PRIDE accession numbers 2354–2378 and 2414.
Contact: hijikata@rcai.riken.jp Supplementary data are available at online.
language:
source:
identifier: ISSN: 1367-4803 ; E-ISSN: 1460-2059 ; DOI: 10.1093/bioinformatics/btm430
fulltext: fulltext
issn:
  • 1367-4803
  • 13674803
  • 1460-2059
  • 14602059
url: Link


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titleConstruction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
creatorHijikata, 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
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titleConstruction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
description
0Motivation: 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.
1The database, named RefDIC (erence genomics atabase of mmune ells), 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.
2All raw data and information can be accessed from . The microarray data is also available at under CIBEX accession no. CBX19, and under PRIDE accession numbers 2354–2378 and 2414.
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4Supplementary data are available at online.
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titleConstruction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
authorHijikata, 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
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32Tanaka, Masato
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37Watarai, Hiroshi
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atitleConstruction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
jtitleBioinformatics
risdate200711
volume23
issue21
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doi10.1093/bioinformatics/btm430
date2007-11