SRA Tool: SOFL-Based Requirements Analysis Tool

Mat, Abdul Rahman; Masli, Azman Bujang; Burhan, N. H.; Liu, S.

doi:10.1007/978-3-642-37371-8_25

Cited by 1 publication

(1 citation statement)

References 4 publications

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“…The Sequence Read Archive (SRA) files and clinical information of the selected datasets were downloaded from SRA Run Selector ( https://www.ncbi.nlm.nih.gov/Traces/study ) for further analysis in the Linux operating system. Paired-end SRA files were divided into two single-end fastq compressed files using the Fastq-dump function in sra-tools software (version 2.10.0) [ 18 ]. After adapter trimming using Trim Galore (version 0.6.4) ( www.bioinformatics.babraham.ac.uk/projects/trim_galore ) and removal of low-quality reads (N base % > 5% or Q20 < 80%), the filtered reads were aligned to the hg19 reference genome/transcriptome from the UCSC Genome Browser (genome.ucsc.edu) with the BWA-MEM function in BWA software (version 0.7.17) [ 19 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of hsa_circ_0002024 as a prognostic competing endogenous RNA (ceRNA) through the hsa_miR_129-5p/Anti-Silencing Function 1B Histone Chaperone (ASF1B) axis in renal cell carcinoma

Chen

Huang

et al. 2021

Bioengineered

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We aimed to identify novel circular RNAs (circRNAs) as prognostic competing endogenous RNAs (ceRNAs) to serve as genetic biomarkers and therapeutic targets for renal cell carcinoma (RCC). High-throughput sequencing data of circRNAs from Gene Expression Omnibus (GEO) and of microRNAs (miRNAs) and messenger RNAs (mRNAs) from The Cancer Genome Atlas (TCGA) were retrieved to identify differentially expressed RNAs (DERNAs). DEmRNAs were subjected to weighted gene coexpression network analysis (WGCNA) to identify prognostic DEmRNA (proDEmRNA) modules. Overlapping DEcircRNA-DEmiRNA and DEmiRNA-proDEmRNA interactions among the TargetScan, miRanda and RNAhybrid databases were constructed and identified. The circRNA-miRNA-mRNA ceRNA network was constructed using mutual DEmiRNAs in two interaction networks as nodes. mRNAs validated as significantly overexpressed in RCC by Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA) and quantitative polymerase chain reaction (q-PCR), along with the correlative miRNAs, were used for survival analysis. Finally, a ceRNA network with 13 upregulated circRNAs, 8 downregulated miRNAs and 21 upregulated mRNAs was constructed, in which Anti-Silencing Function 1B Histone Chaperone (ASF1B) and Forkhead Box M1 (FOXM1) were considered significant by Oncomine, GEPIA and q-PCR. Survival analysis showed that ASF1B, FOXM1 and hsa_miR_1254 were significantly negatively correlated but hsa_miR_129-5p was positively correlated with overall survival time. Exploration of the ceRNA network revealed the prognostic hsa_circ_0002024/hsa_miR_129-5p/ASF1B axis. Therefore, hsa_-circ_0002024 was identified as a prognostic ceRNA that might sponge hsa_miR_129-5p to regulate ASF1B and affect RCC prognosis. However, further validation is needed.

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Section: Methodsmentioning

confidence: 99%