SoyNcRNAExp

Welcome to SoyNcRNAExp

SoyNcRNAExp is a resource for soybean non-coding RNA expression and co-expression network analysis based on 1,263 RNA-seq libraries and 333 sRNA-seq libraries. The 18,845 ncRNAs in SoyNcRNAExp include 4,179 long non-coding RNAs (lncRNAs), 451 PHAS/TAS genes, 1,245 microRNAs (miRNAs) and 12,970 phased siRNAs (phasiRNAs). In addition, 3,747 transcription factors (TFs), 135 RNA-binding proteins (RBPs) and 52,297 protein-coding genes were also collected to expand ncRNA-centered networks. SoyNcRNAExp contains four major functionalities: ncRNA expression, ncRNA differential expression, ncRNA mining, and ncRNA co-expression.

Non-coding RNA	long non-coding RNA	microRNA	phased siRNA	PHAS gene
Number	4,179	1,245	12,970	451

Gene	Transcription factor	RNA-binding protein	protein-coding gene
Number	3,747	135	52,297

Tissue expression information

A total of 25 different tissues are involved in RNA-seq libraries, and their sample numbers are distributed as follows.

A total of 22 different tissues are involved in sRNA-seq libraries, and their sample numbers are distributed as follows.

Co-Expression information

1,263 RNA-seq libraries were used to calculate the expression levels of genes, including lncRNAs, PHAS genes, TFs, RBPs, and protein-coding genes, while 333 sRNA-seq libraries were used to calculate the expression levels of small RNAs, including microRNA and phased siRNA. 141 libraries are containing both RNA-seq and sRNA-seq, which are used for co-expression analysis.

Differential expression information

A total of 23 differential conditions are involved in the RNA-seq libraries, which contain the number of differential analysis groups as shown in the figure below.

A total of 4 differential conditions are involved in the sRNA-seq libraries, which contain the number of differential analysis groups as shown in the figure below.

Citation:

Zhu X, Zhang B, Gao F, Huang F, Zhang H, Huang J. A Soybean Non-coding RNA Mining and Co-expression Resource Based on 1,596 RNA-seq and Small RNA-seq Libraries. Plant Physiol. 2022;kiac222. doi:10.1093/plphys/kiac222