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Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

Rice Expression Database (RED) 2.0: an updated rice database integrating diverse RNA expression profiles based on the telomere-to-telomere reference genome

  • Zihan Wang1,2,3,4,5
  • Mingzhu Li1,2,3
  • Ming Chen1,2,3
  • Zhao Li1,2,3
  • Dechang Yang1,2,3
  • Dong Zou1,2,3
  • Zhang Zhang1,2,3,4,5
  • Tianyi Xu1,2,3
5 affiliations
  1. 1National Genomics Data Center, China National Center for Bioinformation , Beijing 100101 ,
  2. 2Beijing Key Laboratory of Intelligent Governance and Application of Biological Big Data, China National Center for Bioinformation , Beijing 100101 ,
  3. 3Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 ,
  4. 4University of Chinese Academy of Sciences , Beijing 100049 ,
  5. 5Sino-Danish College, University of Chinese Academy of Sciences , Beijing 100049 ,
Open at sourcePDFDOICite

Abstract

Rice Expression Database (RED) is a rice gene expression database derived from large-scale RNA-seq data across different tissues and experimental conditions. Here, we present RED 2.0 (https://ngdc.cncb.ac.cn/red) with significant updates and enhancements. Specifically, RED 2.0 contains 357 projects covering 6471 bulk RNA-seq experiments across 18 tissues and 78 single-cell RNA-seq experiments comprising 984 495 cells. All projects are further manually curated and grouped into diverse biological contexts, including abiotic stress, biotic stress, hormone, development, genotype, and anatomy. Notably, based on the telomere-to-telomere assembly of the Nipponbare genome, RED 2.0 incorporates comprehensive expression profiles for 57 359 protein-coding genes (67 818 transcripts), 16 522 long non-coding RNA genes (47 396 transcripts), and 79 007 circular RNAs. In addition, it is equipped with online tools for differential expression analysis, functional enrichment analysis, co-expression network construction, and genome browser. Collectively, RED 2.0 provides a comprehensive expression landscape for both coding and non-coding genes across diverse conditions, serving as an important resource for rice functional genomics and molecular breeding.

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Cite

BibTeXRIS
BibTeX
@article{wang2026rice,
  title = {{Rice Expression Database (RED) 2.0: an updated rice database integrating diverse RNA expression profiles based on the telomere-to-telomere reference genome}},
  author = {Zihan Wang and Mingzhu Li and Ming Chen and Zhao Li and Dechang Yang and Dong Zou and Zhang Zhang and Tianyi Xu},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1064},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1064/9002624},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - Rice Expression Database (RED) 2.0: an updated rice database integrating diverse RNA expression profiles based on the telomere-to-telomere reference genome
AU  - Zihan Wang
AU  - Mingzhu Li
AU  - Ming Chen
AU  - Zhao Li
AU  - Dechang Yang
AU  - Dong Zou
AU  - Zhang Zhang
AU  - Tianyi Xu
PY  - 2026
DA  - 2026/10/27
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1064
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1064/9002624
AB  - Rice Expression Database (RED) is a rice gene expression database derived from large-scale RNA-seq data across different tissues and experimental conditions. Here, we present RED 2.0 (https://ngdc.cncb.ac.cn/red) with significant updates and enhancements. Specifically, RED 2.0 contains 357 projects covering 6471 bulk RNA-seq experiments across 18 tissues and 78 single-cell RNA-seq experiments comprising 984 495 cells. All projects are further manually curated and grouped into diverse biological contexts, including abiotic stress, biotic stress, hormone, development, genotype, and anatomy. Notably, based on the telomere-to-telomere assembly of the Nipponbare genome, RED 2.0 incorporates comprehensive expression profiles for 57 359 protein-coding genes (67 818 transcripts), 16 522 long non-coding RNA genes (47 396 transcripts), and 79 007 circular RNAs. In addition, it is equipped with online tools for differential expression analysis, functional enrichment analysis, co-expression network construction, and genome browser. Collectively, RED 2.0 provides a comprehensive expression landscape for both coding and non-coding genes across diverse conditions, serving as an important resource for rice functional genomics and molecular breeding.
SN  - 0305-1048
SN  - 1362-4962
ER  -