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


BACKGROUND
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.
Hijikata
Atsushi
A
RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
Kitamura
Hiroshi
H
Kimura
Yayoi
Y
Yokoyama
Ryo
R
Aiba
Yuichi
Y
Bao
Yanyuan
Y
Fujita
Shigeharu
S
Hase
Koji
K
Hori
Shohei
S
Ishii
Yasuyuki
Y
Kanagawa
Osami
O
Kawamoto
Hiroshi
H
Kawano
Kazuya
K
Koseki
Haruhiko
H
Kubo
Masato
M
Kurita-Miki
Ai
A
Kurosaki
Tomohiro
T
Masuda
Kyoko
K
Nakata
Mitsumasa
M
Oboki
Keisuke
K
Ohno
Hiroshi
H
Okamoto
Mariko
M
Okayama
Yoshimichi
Y
O-Wang
Jiyang
J
Saito
Hirohisa
H
Saito
Takashi
T
Sakuma
Machie
M
Sato
Katsuaki
K
Sato
Kaori
K
Seino
Ken-ichiro
K
Setoguchi
Ruka
R
Tamura
Yuki
Y
Tanaka
Masato
M
Taniguchi
Masaru
M
Taniuchi
Ichiro
I
Teng
Annabelle
A
Watanabe
Takeshi
T
Watarai
Hiroshi
H
Yamasaki
Sho
S
Ohara
Osamu
O
D000818:Animals; D003628:Database Management Systems; D016208:Databases, Factual; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D008214:Lymphocytes / Q000276:immunology*; D020543:Proteome / Q000276:immunology*; D018511:Systems Integration; D014157:Transcription Factors / Q000276:immunology*
D020543:Proteome; D014157:Transcription Factors