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Although a huge amount of mammalian genomic data does become publicly available, …


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

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

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

Bioinformatics 2007 23(21):2934-2941; doi:10.1093/bioinformatics/btm430. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License.

 

Abstract

Motivation: Although a huge amount of mammalian genomic datadoes become publicly available, there are still hurdles forbiologists to overcome before such data can be fully exploited.One of the challenges for gaining biological insight from genomicdata has been the inability to cross-reference transcriptomicand proteomic data using a single informational platform. Toaddress this, we constructed an open-access database that enabledus to cross-reference transcriptomic and proteomic data obtainedfrom immune cells.

Results: The database, named RefDIC (Reference genomics Databaseof Immune Cells), currently contains: (i) quantitative mRNAprofiles for human and mouse immune cells/tissues obtained usingAffymetrix GeneChip technology; (ii) quantitative protein profilesfor 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 mRNAand protein profiles of immune cells. RefDIC is the first open-accessdatabase for immunogenomics and serves as an important information-sharingplatform, enabling a focused genomic approach in immunology.

Availability: All raw data and information can be accessed fromhttp://refdic.rcai.riken.jp/. The microarray data is also availableat http://cibex.nig.ac.jp/and http://www.ebi.ac.uk/pride/ under PRIDE accession numbers2354–2378 and 2414. under CIBEX accession no. CBX19,

 


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