RESUMO
Circular RNAs are newly identified RNAs that regulate gene expression and execute various biological activities. Facet joint osteoarthritis (FJOA) is a severe facet joint cartilage degeneration disease that induces chronic low back pain to a larger population. The molecular mechanisms of FJOA, especially the presence and changes of circular RNAs in FJOA have not been investigated. In the current study, we analyzed RNA deep sequencing outcomes from healthy control group and FJOA group, identified and annotated circular RNAs, and determined the expressions of circular RNAs. Differentially expressed circular RNAs in the FJOA group were then screened and the host genes of these differentially expressed circular RNAs were functional analyzed by Gene Ontology (GO), Kyoto Enrichment of Genes and Genomes (KEGG), and protein-protein interaction network analysis. Seven circRNAs were arbitrarily selected to confirm the trustworthiness of these profiles by quantitative qRT-PCR. The potential binding sites of microRNAs (miRNAs) and identified circular RNAs were also predicted. Our current study provided valuable bioinformation regarding circular RNAs in FJOA and expanded our knowledge of FJOA.
Assuntos
Osteoartrite/genética , RNA/genética , Transcriptoma , Articulação Zigapofisária/metabolismo , Regulação da Expressão Gênica , Humanos , Osteoartrite/metabolismo , Osteoartrite/patologia , Mapas de Interação de Proteínas , RNA Circular , Análise de Sequência de RNA , Articulação Zigapofisária/patologiaRESUMO
With the widespread implementation of next-generation sequencing (NGS) technologies, millions of sequences have been produced. A lot of databases were created to store and organize the high-throughput sequencing data. Numerous analysis software programs and tools have been developed over the past years. Most of them use specific formats for data representation and storage. Data interoperability becomes a crucial challenge and many tools have been developed to convert NGS data from one format to another. However, most of them were developed for specific and limited formats. Here, we present NGS-FC (Next-Generation Sequencing Format Converter), which provides a framework to support the conversion between several formats. It supports 14 formats now and provides interfaces to enable users to improve the existing converters and add new ones. Moreover, NGS-FC achieved the overall competitive performance in comparison with some existing converters in terms of RAM usage and running time. The software is written in Java and can be executed standalone. The source code and documentation are freely available at http://sysbio.suda.edu.cn/NGS-FC.