RiceNCexp: a rice non-coding RNA co-expression atlas based on massive RNA-seq and small-RNA seq data.

Baoyi Zhang, Yuhan Fei, Jiejie Feng, Xueai Zhu, Rui Wang, Hanqing Xiao, Hongsheng Zhang, Ji Huang
Author Information
  1. Baoyi Zhang: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. ORCID
  2. Yuhan Fei: MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
  3. Jiejie Feng: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
  4. Xueai Zhu: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. ORCID
  5. Rui Wang: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
  6. Hanqing Xiao: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
  7. Hongsheng Zhang: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
  8. Ji Huang: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. ORCID

Abstract

Non-coding RNAs (ncRNAs) play important roles in regulating expression of protein-coding genes. Although gene expression databases have emerged in a timely manner, a comprehensive expression database for ncRNAs is still lacking. Herein, we constructed a rice ncRNA co-expression atlas (RiceNCexp), based on 491 RNA-seq and 274 small RNA (sRNA)-seq datasets. RiceNCexp hosts four types of ncRNAs, namely lncRNAs, PHAS genes, miRNAs, and phasiRNAs. RiceNCexp provides comprehensive expression information for rice ncRNAs in 22 tissues/organs, an efficient tau-based mining tool for tissue-specific ncRNAs, and the robust co-expression analysis among ncRNAs or between ncRNAs and protein-coding genes, based on 116 pairs of RNA-seq and sRNA-seq libraries from the same experiments. In summary, RiceNCexp is a user-friendly and comprehensive rice ncRNA co-expression atlas and can be freely accessed at https://cbi.njau.edu.cn/RiceNCexp/.

Keywords

Grants

  1. /Fundamental Research Funds for the Central Universities
  2. [2021]009/Jiangsu Provincial Seed Industry Revitalization Project
  3. KYCX21_0561/Postgraduate Research & Practice Innovation Program of Jiangsu Province

MeSH Term

RNA, Long Noncoding
Oryza
Sequence Analysis, RNA
RNA-Seq
RNA, Untranslated
MicroRNAs

Chemicals

RNA, Long Noncoding
RNA, Untranslated
MicroRNAs

Links to CNCB-NGDC Resources

Database Commons: DBC008220 (RiceNCexp)

Word Cloud

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