Lists of computational tools and bioinformatics resources for analysis of personal mutanomes in cancer
| Names | Description | Website | Refs | |
|---|---|---|---|---|
| Cancer genomics resources | ||||
| TCGA and GDC | The Cancer Genome Atlas and Genomic Data Commons Data Portal | https://portal.gdc.cancer.gov | Chin et al. (2011) | |
| ICGC | The International Cancer Genome Consortium | https://icgc.org | Milius et al. (2014) | |
| CBioPortal | Providing visualization, analysis and download of large-scale cancer genomics data sets. | http://www.cbioportal.org | Gao et al. (2013) | |
| COSMIC | Comprehensive resources for curating somatic mutations | http://cancer.sanger.ac.uk/cosmic | Forbes et al. (2015) | |
| Bioinformatics resources for protein structures | ||||
| PDB | The PDB is the global archive for experimentally determined, atomic-level three-dimensional structures of proteins, DNA, and RNA. | https://www.rcsb.org/ | Rose et al. (2017) | |
| Interactome3D | Manually curated protein-protein interactions with known three-dimensional structure information. | http://interactome3d.irbbarcelona.org | Mosca et al. (2013) | |
| dSysMap | dSysMap is a useful tool to study the network perturbations by genetic variants | http://dsysmap.irbbarcelona.org/ | Mosca et al. (2015) | |
| Interactome INSIDER | An integrative structural and genomic resource for functional exploration of human disease mutations at multiple-scale, proteome-wide human interactome | http://interactomeinsider.yulab.org | Meyer et al. (2018) | |
| Mutational clustering tools on protein structures | ||||
| AlloDriver | Detect druggable mutations via dysregulation of protein allosteric functions. | NA | Shen et al. (2017) | |
| Cancer3D | A useful tool to explore potential cancer drivers or pharmacogenomic biomarkers using protein structure information. | http://cancer3d.org/ | Porta-Pardo et al. (2015) | |
| CLUMPS | Assess the significance of mutational clustering in a given 3D structure. | NA | Kamburov et al. (2015) | |
| HotSpot3D | Detect mutation–mutation and mutation–drug clusters using three-dimensional protein structures. | NA | Niu et al. (2016) | |
| KNMPx | Detect a kinome-wide pharmacogenomic biomarkers via rewiring phosphorylation-related signaling networks and drug sensitivity/resistance | NA | Zhao et al. (2017) | |
| ReKINect | Detect network-attacking mutations in phosphorylation-based signaling networks. | http://rekinect.science/ | Creixell et al. (2015) | |
| SGDriver | A structural genomics-based method that detects mutation clustering on protein–ligand binding site residues via a Bayes inference statistical framework. | NA | Zhao et al. (2016) | |