ArticleNucleic acids research2018
RISE: a database of RNA interactome from sequencing experiments.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed, 113 citations in OpenAlex.
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- The role of low-complexity repeats in RNA-RNA interactions and a deep learning framework for duplex prediction.Nature communications · 2026Article
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- Identification and Sequence Characterization of Semi-extractable RNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computational limitations and future needs to unravel the full potential of 2'-O-methylation and C/D box snoRNAs.RNA biology · 2025Review
- Role of Compensatory miRNA Networks in Cognitive Recovery from Heart Failure.Non-coding RNA · 2025Article
- DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA-RNA interaction data.Nucleic acids research · 2025Article
- Complete stranded RNA profiling during early mouse gonad development.NAR molecular medicine · 2025Article
- Identification of Genomic Instability-Associated LncRNAs as Potential Therapeutic Targets in Lung Adenocarcinoma.Cancers · 2025Article
- Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2025Article
- Footprints in the Sno: investigating the cellular and molecular mechanisms of SNORD116.Open biology · 2025Review
- MicroRNA in neuroexosome as a potential biomarker for HIV-associated neurocognitive disorders.Journal of neurovirology · 2025Article
- Transcriptomic profiling and machine learning reveal novel RNA signatures for enhanced molecular characterization of Hashimoto's thyroiditis.Scientific reports · 2025Article
- Computational Prediction of Gene Regulation by lncRNAs.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Review of the Different Outcomes Produced by Genetic Knock Out of the Long Non-coding microRNA-host-gene MIR22HGMicroRNA (Shariqah, United Arab Emirates) · 2025Review
- The plasma miRNAome in ADNI: Signatures to aid the detection of at-risk individuals.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- Defective mitochondrial COX1 translation due to loss of COX14 function triggers ROS-induced inflammation in mouse liver.Nature communications · 2024Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast. While most existing RNA databases mainly contain interactions of miRNA targeting, notably, more than half of the RRIs in RISE are among mRNA and long non-coding RNAs. We compared different RRI datasets in RISE and found limited overlaps in interactions resolved by different techniques and in different cell lines. It may suggest technology preference and also dynamic natures of RRIs. We also analyzed the basic features of the human and mouse RRI networks and found that they tend to be scale-free, small-world, hierarchical and modular. The analysis may nominate important RNAs or RRIs for further investigation. Finally, RISE provides a Circos plot and several table views for integrative visualization, with extensive molecular and functional annotations to facilitate exploration of biological functions for any RRI of interest.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.