Table 2.
A list of publicly available bioinformatics software used to identify candidate miRNAs and their gene targets, with particular relevance to ovarian cancer.
| Tool | Web Address | Function |
|---|---|---|
| Target Scan Human 8.0 | www.targetscan.org/vert_80 (accessed on 7 November 2022) | Search for predicted miRNA targets |
| metaMIR V 1.1.0 | http://rna.informatik.uni-freiburg.de/metaMIR/Input.jsp (accessed on 7 November 2022) | Predict interactions between miRNAs and clusters of genes in human |
| OncomiR | http://www.oncomir.org/ (accessed on 7 November 2022) | WashU Pan-Cancer miRNome Atlas exploring pan-cancer microRNA dysregulation |
| GeneNet V 3.0.2 | http://www.oncomir.org/ (accessed on 7 November 2022) | R package for learning high-dimensional dependency networks from genomic data |
| Cytoscape V3.7.1 | https://cytoscape.org/ (accessed on 7 November 2022) | Network data integration, analysis and visualization |
| DiffCorr V0.4.2 | https://sourceforge.net/projects/diffcorr/ (accessed on 7 November 2022) | R package to analyze differential correlations biological networks |
| STRING V11.5 | https://string-db.org/ (accessed on 7 November 2022) | Protein–protein interaction networks Functional enrichment analysis |
| Webgestalt V2019 | http://www.webgestalt.org/ (accessed on 7 November 2022) | Gene list over-representation analysis |