Baoyi Zhang: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. ORCID
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.
Jiejie Feng: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
Xueai Zhu: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. ORCID
Rui Wang: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
Hanqing Xiao: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
Hongsheng Zhang: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
Ji Huang: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. ORCID
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/.
