Dataset Information

A comprehensive overview and evaluation of circular RNA detection tools.

ABSTRACT: Circular RNA (circRNA) is mainly generated by the splice donor of a downstream exon joining to an upstream splice acceptor, a phenomenon known as backsplicing. It has been reported that circRNA can function as microRNA (miRNA) sponges, transcriptional regulators, or potential biomarkers. The availability of massive non-polyadenylated transcriptomes data has facilitated the genome-wide identification of thousands of circRNAs. Several circRNA detection tools or pipelines have recently been developed, and it is essential to provide useful guidelines on these pipelines for users, including a comprehensive and unbiased comparison. Here, we provide an improved and easy-to-use circRNA read simulator that can produce mimicking backsplicing reads supporting circRNAs deposited in CircBase. Moreover, we compared the performance of 11 circRNA detection tools on both simulated and real datasets. We assessed their performance regarding metrics such as precision, sensitivity, F1 score, and Area under Curve. It is concluded that no single method dominated on all of these metrics. Among all of the state-of-the-art tools, CIRI, CIRCexplorer, and KNIFE, which achieved better balanced performance between their precision and sensitivity, compared favorably to the other methods.

SUBMITTER: Zeng X

PROVIDER: S-EPMC5466358 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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A comprehensive overview and evaluation of circular RNA detection tools.

Zeng Xiangxiang X Lin Wei W Guo Maozu M Zou Quan Q

PLoS computational biology 20170608 6

Circular RNA (circRNA) is mainly generated by the splice donor of a downstream exon joining to an upstream splice acceptor, a phenomenon known as backsplicing. It has been reported that circRNA can function as microRNA (miRNA) sponges, transcriptional regulators, or potential biomarkers. The availability of massive non-polyadenylated transcriptomes data has facilitated the genome-wide identification of thousands of circRNAs. Several circRNA detection tools or pipelines have recently been develop ...[more]

PMID: 28594838

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Project description:BackgroundCircular RNAs (circRNAs) have been shown to play important regulatory roles in a range of both pathological and physiological contexts, but their functions in the context of skin aging remain to be clarified. In the present study, we therefore, profiled circRNA expression profiles in four pairs of aged and non-aged skin samples to identify identifying differentially expressed circRNAs that may offer clinical value as biomarkers of the skin aging process.MethodsWe utilized an RNA-seq to profile the levels of circRNAs in eyelid tissue samples, with qRT-PCR being used to confirm these RNA-seq results, and with bioinformatics approaches being used to predict downstream target miRNAs for differentially expressed circRNAs.ResultsIn total, we identified 571 circRNAs with 348 and 223 circRNAs being up and downregulated that were differentially expressed in aged skin samples compared to young skin samples. The top 10 upregulated circRNAs in aged skin sample were hsa_circ_0123543, hsa_circ_0057742, hsa_circ_0088179, hsa_circ_0132428, hsa_circ_0094423, hsa_circ_0008166, hsa_circ_0138184, hsa_circ_0135743, hsa_circ_0114119, and hsa_circ_0131421. The top 10 reduced circRNAs were hsa_circ_0101479, hsa_circ_0003650, hsa_circ_0004249, hsa_circ_0030345, hsa_circ_0047367, hsa_circ_0055629, hsa_circ_0062955, hsa_circ_0005305, hsa_circ_0001627, and hsa_circ_0008531. Functional enrichment analyses revealed the potential functionality of these differentially expressed circRNAs. The top 3 enriched gene ontology (GO) terms of the host genes of differentially expressed circRNAs are regulation of GTPase activity, positive regulation of GTPase activity and autophagy. The top 3 enriched KEGG pathway ID are Lysine degradation, Fatty acid degradation and Inositol phosphate metabolism. The top 3 enriched reactome pathway ID are RAB GEFs exchange GTP for GDP on RABs, Regulation of TP53 Degradation and Regulation of TP53 Expression and Degradation. Six circRNAs were selected for qRT-PCR verification, of which 5 verification results were consistent with the sequencing results. Moreover, targeted miRNAs, such as hsa-miR-588, hsa-miR-612, hsa-miR-4487, hsa-miR-149-5p, hsa-miR-494-5p were predicted for circRna-miRna interaction networks.ConclusionOverall, these results offer new insights into circRNA expression profiles, potentially highlighting future avenues for research regarding the roles of these circRNAs in the context of skin aging.

Project description:ObjectivesThe Network on the Coordination and Harmonisation of European Occupational Cohorts (OMEGA-NET) was set up to enable optimization of the use of industrial and general population cohorts across Europe to advance aetiological research. High-quality harmonized exposure assessment is crucial to derive comparable results and to enable pooled analyses. To facilitate a harmonized research strategy, a concerted effort is needed to catalogue available occupational exposure information. We here aim to provide a first comprehensive overview of exposure assessment tools that could be used for occupational epidemiological studies.MethodsAn online inventory was set up to collect meta-data on exposure assessment tools. Occupational health researchers were invited via newsletters, editorials, and individual e-mails to provide details of job-exposure matrices (JEMs), exposure databases, and occupational coding systems and their associated crosswalks to translate codes between different systems, with a focus on Europe.ResultsMeta-data on 36 general population JEMs, 11 exposure databases, and 29 occupational coding systems from more than 10 countries have been collected up to August 2021. A wide variety of exposures were covered in the JEMs on which data were entered, with dusts and fibres (in 14 JEMs) being the most common types. Fewer JEMs covered organization of work (5) and biological factors (4). Dusts and fibres were also the most common exposures included in the databases (7 out of 11), followed by solvents and pesticides (both in 6 databases).ConclusionsThis inventory forms the basis for a searchable web-based database of meta-data on existing occupational exposure information, to support researchers in finding the available tools for assessing occupational exposures in their cohorts, and future efforts for harmonization of exposure assessment. This inventory remains open for further additions, to enlarge its coverage and include newly developed tools.

Dataset Information

A comprehensive overview and evaluation of circular RNA detection tools.

Publications

A comprehensive overview and evaluation of circular RNA detection tools.

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