Skip Navigation


Bioinformatics Advance Access originally published online on September 24, 2007
Bioinformatics 2007 23(21):2934-2941; doi:10.1093/bioinformatics/btm430
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary data
Right arrowOA All Versions of this Article:
23/21/2934    most recent
btm430v2
btm430v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (3)
Google Scholar
Right arrow Articles by Hijikata, A.
Right arrow Articles by Ohara, O.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hijikata, A.
Right arrow Articles by Ohara, O.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Atsushi Hijikata 1, Hiroshi Kitamura 1, Yayoi Kimura 1, Ryo Yokoyama 1, Yuichi Aiba 1, Yanyuan Bao 1, Shigeharu Fujita 1, Koji Hase 1, Shohei Hori 1, Yasuyuki Ishii 1, Osami Kanagawa 1, Hiroshi Kawamoto 1, Kazuya Kawano 1, Haruhiko Koseki 1, Masato Kubo 1, Ai Kurita-Miki 1, Tomohiro Kurosaki 1, Kyoko Masuda 1, Mitsumasa Nakata 1, Keisuke Oboki 1, Hiroshi Ohno 1, Mariko Okamoto 1, Yoshimichi Okayama 1, Jiyang O-Wang 1, Hirohisa Saito 1, Takashi Saito 1, Machie Sakuma 1, Katsuaki Sato 1, Kaori Sato 1, Ken-ichiro Seino 1, Ruka Setoguchi 1, Yuki Tamura 1, Masato Tanaka 1, Masaru Taniguchi 1, Ichiro Taniuchi 1, Annabelle Teng 1, Takeshi Watanabe 1, Hiroshi Watarai 1, Sho Yamasaki 1 and Osamu Ohara 1,2,*

1RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 and 2Department of Human Genome Technology, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan

*To whom correspondence should be addressed.


  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.

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.

Contact: hijikata{at}rcai.riken.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on March 7, 2007; revised on July 31, 2007; accepted on August 17, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
S. Keerthikumar, R. Raju, K. Kandasamy, A. Hijikata, S. Ramabadran, L. Balakrishnan, M. Ahmed, S. Rani, L. D. N. Selvan, D. S. Somanathan, et al.
RAPID: Resource of Asian Primary Immunodeficiency Diseases
Nucleic Acids Res., October 8, 2008; (2008) gkn682v1.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
H. Kitamura, M. Ito, T. Yuasa, C. Kikuguchi, A. Hijikata, M. Takayama, Y. Kimura, R. Yokoyama, T. Kaji, and O. Ohara
Genome-wide identification and characterization of transcripts translationally regulated by bacterial lipopolysaccharide in macrophage-like J774.1 cells
Physiol Genomics, October 8, 2008; 33(1): 121 - 132.
[Abstract] [Full Text] [PDF]

Home page
 J. Immunol.Home page
H. Hara, C. Ishihara, A. Takeuchi, L. Xue, S. W. Morris, J. M. Penninger, H. Yoshida, and T. Saito
Cell Type-Specific Regulation of ITAM-Mediated NF-{kappa}B Activation by the Adaptors, CARMA1 and CARD9
J. Immunol., July 15, 2008; 181(2): 918 - 930.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.