Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice

Lin Xia; Dong Zou; Jian Sang; Xingjian Xu; Hongyan Yin; Mengwei Li; Shuangyang Wu; Songnian Hu; Lili Hao; Zhang Zhang

doi:10.1016/j.jgg.2017.05.003

Volume 44 Issue 5

May 2017

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Article Navigation > Journal of Genetics and Genomics > 2017 > 44(5): 235-241

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Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice

doi: 10.1016/j.jgg.2017.05.003

Lin Xia^{a, b, c, #},
Dong Zou^{a, b, #},
Jian Sang^{a, b, c},
Xingjian Xu^{a, b, c},
Hongyan Yin^{a, b, c},
Mengwei Li^{a, b, c},
Shuangyang Wu^{a, c},
Songnian Hu^{a, c, d},
Lili Hao^{a, b},
Zhang Zhang^{a, b, c, d}

a
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
b
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
c
University of Chinese Academy of Sciences, Beijing 100049, China
d
Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China

More Information

Corresponding author: E-mail address: haolili@big.ac.cn (Lili Hao); E-mail address: zhangzhang@big.ac.cn (Zhang Zhang)
Received Date: 2017-01-03
Accepted Date: 2017-05-02
Rev Recd Date: 2017-04-24

Available Online: 2017-05-04

Publish Date: 2017-05-20

Abstract

Abstract

Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community. Here, we present RED (Rice Expression Database; http://expression.ic4r.org), an integrated database of rice gene expression profiles derived entirely from RNA-Seq data. RED features a comprehensive collection of 284 high-quality RNA-Seq experiments, integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments. Based on massive expression profiles, RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest. Besides, it provides user-friendly web interfaces for querying, browsing and visualizing expression profiles of concerned genes. Together, as a core resource in BIG Data Center, RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.
- Rice expression database,
- Expression profiles,
- Housekeeping gene,
- Tissue-specific gene,
- Co-expression network

These authors contributed equally to this work.

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References(21)

References

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