ArticleAdvances in experimental medicine and biology2025
Circular RNA Identification and Characterization with CircRNAFlow: A Bioinformatics Approach.
Article in Advances in experimental medicine and biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circular RNAs (circRNAs) play various roles in gene regulation and are known to be associated with the development of disease. They can act as microRNA sponges, interact with RNA-binding proteins, and even contain open reading frames (ORFs) that are translated to generate proteins. Scientists hope to better understand these covalently closed ring-like structures as they are not well-characterized.Here, we present CircRNAFlow, a free and open-source Nextflow-based pipeline for in silico circRNA identification and characterization. This next-generation sequencing (NGS) pipeline takes paired-end FASTQ files as input and produces tables and graphical images that report identified circRNAs and their corresponding characterizations. Reports include CircTest to compare circRNA expression to host gene expression and across groups. Characterization includes ClusterProfiler, CRAFT (CircRNA Function prediction Tool), and deepTarget, which explore the regulatory roles of identified circRNAs.In this chapter, we discuss the bioinformatics analyses carried out by the incorporated third-party software of CircRNAFlow [namely, FastQC, Flexbar, Bowtie2, STAR (Spliced Transcripts Alignment to a Reference), DCC (detect circRNAs from chimeric reads), CircTest, CRAFT, ClusterProfiler, and deepTarget]. This chapter, along with a companion GitHub repository, provides a tutorial on CircRNAFlow, including installation, running the software, and interpretation of the outputs. This chapter also provides some troubleshooting tips.
Indexed as
Identifiers
40886271What OpenQuestion holds
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.