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

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

J Genet Genomics. 2017 May 20;44(5):235-241. doi: 10.1016/j.jgg.2017.05.003. Epub 2017 May 4.

Authors

Lin Xia¹, Dong Zou², Jian Sang¹, Xingjian Xu¹, Hongyan Yin¹, Mengwei Li¹, Shuangyang Wu³, Songnian Hu⁴, Lili Hao⁵, Zhang Zhang⁶

Affiliations

¹ CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
² CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
³ CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
⁴ CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China.
⁵ CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: haolili@big.ac.cn.
⁶ CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China. Electronic address: zhangzhang@big.ac.cn.

PMID: 28529082
DOI: 10.1016/j.jgg.2017.05.003

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.

Keywords: Co-expression network; Expression profiles; Housekeeping gene; Rice expression database; Tissue-specific gene.

MeSH terms

Databases, Nucleic Acid*
Gene Expression Profiling*
Genes, Plant / genetics
Oryza / genetics*
Oryza / growth & development