RSVdb: a comprehensive database of transcriptome RNA structure.
Haopeng YuYi ZhangQing SunHuijie GaoShiheng TaoPublished in: Briefings in bioinformatics (2021)
RNA fulfills a crucial regulatory role in cells by folding into a complex RNA structure. To date, a chemical compound, dimethyl sulfate (DMS), has been developed to probe the RNA structure at the transcriptome level effectively. We proposed a database, RSVdb (https://taolab.nwafu.edu.cn/rsvdb/), for the browsing and visualization of transcriptome RNA structures. RSVdb, including 626 225 RNAs with validated DMS reactivity from 178 samples in eight species, supports four main functions: information retrieval, research overview, structure prediction and resource download. Users can search for species, studies, transcripts and genes of interest; browse the quality control of sequencing data and statistical charts of RNA structure information; preview and perform online prediction of RNA structures in silico and under DMS restraint of different experimental treatments and download RNA structure data for species and studies. Together, RSVdb provides a reference for RNA structure and will support future research on the function of RNA structure at the transcriptome level.
Keyphrases
- single cell
- nucleic acid
- gene expression
- genome wide
- rna seq
- emergency department
- electronic health record
- oxidative stress
- squamous cell carcinoma
- induced apoptosis
- social media
- mass spectrometry
- deep learning
- single molecule
- living cells
- lymph node metastasis
- case control
- endoplasmic reticulum stress
- cell cycle arrest
- stress induced
- pi k akt
- fluorescent probe