Table 6.
Summary of online resources and tools for identifying cancer driver genes and somatic mutations.
| Name | Description | Link |
|---|---|---|
| GATK-Mutect2 | Genome Analysis Toolkit Mutect2 | https://gatk.broadinstitute.org/hc/en-us |
| VarScan | Variant detection in massively parallel Sequencing data | https://varscan.sourceforge.net/ |
| NeuSomatic | Deep CNNs for accurate somatic mutation detection | https://github.com/bioinform/neusomatic |
| SyRI | Synteny and Rearrangement Identifier | https://github.com/schneebergerlab/syri |
| TSGene | A web resource for tumor suppressor genes | http://bioinfo.mc.vanderbilt.edu/TSGene/ |
| ONGene | A literature-based database for human oncogenes | http://ongene.bioinfo-minzhao.org/ |
| GWAS Catalog | A manually curated resource of all published GWAS and association results | https://www.ebi.ac.uk/gwas |
| GRASP | Genome-Wide Repository of Associations Between SNPs and Phenotypes | https://grasp.nhlbi.nih.gov/Overview.aspx |
| PancanQTL | A user-friendly database to store cis/trans-eQTLs and GWAS-related eQTLs in cancers | http://gong_lab.hzau.edu.cn/PancanQTL/ |
| ABC-GWAS | Analysis of Breast Cancer GWAS | http://education.knoweng.org/abc-gwas/ |
| DriverDBv4 | A database for human cancer driver gene research | http://driverdb.bioinfomics.org/ |
| NCG | Network of cancer genes | http://ncg.kcl.ac.uk/ |
| OncoVar | An integrated database and analysis platform for oncogenic driver variants in cancers | https://oncovar.org/ |
| CNCDatabase | Cornell Non-coding Cancer driver Database | https://cncdatabase.med.cornell.edu |
| IntOGen | Integrative oncogenomics | https://www.intogen.org |
| DriverML | Integrating Rao’s score test and supervised machine learning to identify cancer driver genes | https://github.com/HelloYiHan/DriverML |
| OncodriveCLUST | Identify genes with a significant bias toward mutation clustering within the protein sequence | http://bg.upf.edu/oncodriveclust |
| MuSiC | A pipeline for determining the mutational significance in cancer | |
| MutSigCV | An integrative approach that corrects for variants using patient-specific mutation frequency and spectrum, and gene-specific background mutation model | http://bg.upf.edu/oncodrive |
| OncodriveFM | An approach based on functional impact bias using three well-known methods | https://doi.org/10.5281/zenodo.61372 |
| ContrastRank | A method based on estimating the putative defective rate of each gene in tumor against normal and samples from the 1000 Genomes Project data | |
| PARADIGM | A novel method for detecting consistent pathways in cancers by incorporating patient-specific genetic data into carefully curated NCI pathways | http://sbenz.github.com/Paradigm |
| Helios | An algorithm predicts SMGs by integrating genomic and functional RNAi screening data from primary tumors |
CNNs: Convolutional Neural Networks; DB: Database; eQTLs: Expression quantitative trait loci; GWAS: Genome-wide association studies; NCI: National cancer institute; SNPs: Single nucleotide polymorphisms; SMGs: Significantly Mutated Genes.