Dataset Information

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis.

ABSTRACT:

Background

RNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversity. The automatic detection of RNA-editing from RNA-seq data is computational intensive and limited to small data sets, thus preventing a reliable genome-wide characterisation of such process.

Results

In this work we introduce HPC-REDItools, an upgraded tool for accurate RNA-editing events discovery from large dataset repositories.

Availability

https://github.com/BioinfoUNIBA/REDItools2 .

Conclusions

HPC-REDItools is dramatically faster than the previous version, REDItools, enabling big-data analysis by means of a MPI-based implementation and scaling almost linearly with the number of available cores.

SUBMITTER: Flati T

PROVIDER: S-EPMC7446188 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis.

Flati Tiziano T Gioiosa Silvia S Spallanzani Nicola N Tagliaferri Ilario I Diroma Maria Angela MA Pesole Graziano G Chillemi Giovanni G Picardi Ernesto E Castrignanò Tiziana T

BMC bioinformatics 20200821 Suppl 10

<h4>Background</h4>RNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversity. The automatic detection of RNA-editing from RNA-seq data is computational intensive and limited to small data sets, thus preventing a reliable genome-wide characterisation of such process.<h4>Results</h4>In this work we introduce HPC-REDItools, an upgraded tool for ac ...[more]

PMID: 32838738

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Project description:BackgroundThe abnormal expression of genes is an essential factor affecting the prognosis of cancer. RNA modification is a way of regulating post-transcriptional levels, including m6A, m5C, m1A RNA methylation. Studies have found that RNA methylation regulates tumorigenesis development and stem cell regeneration. However, there are few studies on lung adenocarcinoma. This study aims to explore the clinical value of RNA methylation for lung adenocarcinoma.MethodsWe summarized thirty-one RNA methylation regulators. The training set was obtained from The Cancer Genome Atlas (TCGA) database, and the test set was obtained from the Gene Expression Omnibus (GEO) database. The Wilcoxon test was used to analyze the expression of RNA methylation regulators. We constructed tumor subgroup models and risk models based on the expression of those regulators. Principal component analysis (PCA) and the receiver operating characteristic (ROC) confirmed the accuracy of the models. Real-time polymerase chain reaction (PCR) validates the results in vitro.ResultsMost RNA methylation regulators had distinct expressions in tumor tissues and adjacent tissues (P<0.05). All the models showed high predictive performance (AUC: 0.65-0.82), and the five-year survival of patients in each group was statistically different (P<0.05). The patients in the high-risk group were more likely to have a higher stage, more lymph node metastases, and distant metastases, showing a poor clinical outcome. Patients with high expression of NOP2 or HNRNP were more likely to have a poorly differentiated in vitro experiment.ConclusionsWith our study, we found that the expressions of most RNA methylation regulators were significantly different in cancer and para-cancerous tissues. Different molecular phenotypes constructed by RNA methylation regulators can be independent risk factors for the prognosis of lung adenocarcinoma. Our study demonstrates the critical role of RNA methylation in lung adenocarcinoma, and it is expected to supply a reference for the prognostic stratification and treatment strategy development of lung adenocarcinoma.

Dataset Information

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis.

Background

Results

Availability

Conclusions

Publications

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis.

Similar Datasets

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