ArticleBMC bioinformatics2022
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 22 citations in OpenAlex.
- Toward precision oncology: deciphering the circRNA-EMT axis in cancer and its therapeutic implications.RNA biology · 2026Review
- Circular RNAs in metabolic health: bridging the gap between molecular biology and therapy.Cell death & disease · 2026Review
- From Transcriptome to Therapy: The ncRNA Revolution in Neurodevelopmental Disorders.Brain sciences · 2025Review
- Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis.Briefings in functional genomics · 2025Review
- Validation and in silico function prediction of circtial1 as a novel marker of abnormal lung development in nitrofen-induced congenital diaphragmatic hernia (CDH).Pediatric surgery international · 2024Article
- Review
- Article
- CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs.BMC bioinformatics · 2024Article
- FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing.Nucleic acids research · 2024Article
- Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing.Nucleic acids research · 2023Article
- Assessing the impacts of various factors on circular RNA reliability.Life science alliance · 2023Article
- cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities.International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundCircular RNAs (circRNAs) are a class of non-coding RNAs formed by pre-mRNA back-splicing, which are widely expressed in animal/plant cells and often play an important role in regulating microRNA (miRNA) activities. While numerous databases have collected a large amount of predicted circRNA candidates and provided the corresponding circRNA-regulated interactions, a stand-alone package for constructing circRNA-miRNA-mRNA interactions based on user-identified circRNAs across species is lacking.
resultsWe present CircMiMi (circRNA-miRNA-mRNA interactions), a modular, Python-based software to identify circRNA-miRNA-mRNA interactions across 18 species (including 16 animals and 2 plants) with the given coordinates of circRNA junctions. The CircMiMi-constructed circRNA-miRNA-mRNA interactions are derived from circRNA-miRNA and miRNA-mRNA axes with the support of computational predictions and/or experimental data. CircMiMi also allows users to examine alignment ambiguity of back-splice junctions for checking circRNA reliability and examine reverse complementary sequences residing in the sequences flanking the circularized exons for investigating circRNA formation. We further employ CircMiMi to identify circRNA-miRNA-mRNA interactions based on the circRNAs collected in NeuroCirc, a large-scale database of circRNAs in the human brain. We construct circRNA-miRNA-mRNA interactions comprising differentially expressed circRNAs, and miRNAs in autism spectrum disorder (ASD) and cross-species analyze the relevance of the targets to ASD. We thus provide a rich set of ASD-associated circRNA-miRNA-mRNA axes and a useful starting point for investigation of regulatory mechanisms in ASD pathophysiology.
conclusionsCircMiMi allows users to identify circRNA-mediated interactions in multiple species, shedding light on regulatory roles of circRNAs. The software package and web interface are freely available at https://github.com/TreesLab/CircMiMi and http://circmimi.genomics.sinica.edu.tw/ , respectively.
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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.