Table 2.
Summary of resources providing information about kinases and mutations.
| Method | Description | Further information |
|---|---|---|
| UniProt (Consortium, 2007) | General information about proteins, including human protein kinases | http://www.uniprot.org/ |
| PDB (Berman et al., 2000) | Catalog of protein structures, protein kinases widely represented | http://www.rcsb.org/ |
| PDBsum (Laskowski et al., 2005) | Annotation on protein structures | http://www.ebi.ac.uk/pdbsum |
| KinBase (Manning et al., 2002b; Miranda-Saavedra and Barton, 2007) | Hierarchical classification of protein kinases | http://kinase.com/kinbase/ |
| SwissVar (Yip et al., 2007) | Detailed information about mutations present in UniProt | http://swissvar.expasy.org/ |
| COSMIC (Bamford et al., 2004) | Catalog of somatic mutations in cancer | http://www.sanger.ac.uk/perl/genetics/CGP/cosmic |
| Ensembl (Flicek et al., 2011) | Infrastructure for the integrated annotation on chordate and selected eukaryotic genomes | http://www.ensembl.org |
| dbSNP (Sherry et al., 2001) | Annotated catalog of SNPs | http://www.ncbi.nlm.nih.gov/projects/SNP |
| HapMap (Consortium et al., 2010b) | Catalog of common genetic variants in the human genome | www.hapmap.org |
| 1000 Genomes (Consortium et al., 2010c) | Deep catalog of human variations derived from the next-generation sequencing of 1000 people | http://www.1000genomes.org/ |
| TCGA (Network, 2011) | The Cancer Genome Atlas is a collection of genetic variations found in 20 different cancers | http://cancergenome.nih.gov/ |
| ICGC (Consortium et al., 2010a) | The International Cancer Genome Consortium project aims to a comprehensive description of genomic, transcriptomic, and epigenomic changes in 50 tumor types and sub-types | http://www.icgc.org |
| OMIM (Amberger et al., 2011) | Catalog of Mendelian mutations known to cause disease | http://www.ncbi.nlm.nih.gov/omim |
| SAAPdb (Hurst et al., 2009) | Calculation of the structural consequences of mutations | http://www.bioinf.org.uk/saap/db/ |
| SNPeffect 2.0 (Reumers et al., 2006) | A database mapping molecular phenotypic effects of human non-synonymous coding SNPs | http://snpeffect.switchlab.org |
| ModBase (Pieper et al., 2006) | Structural models of mutant proteins | http://salilab.org/modbase |
| TopoSNP (Stitziel et al., 2004) | TopoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association | http://gila.bioengr.uic.edu/snp/toposnp/ |
| MoKCa (Richardson et al., 2009) | Annotated catalog of cancer-associated mutations in protein kinases | http://strubiol.icr.ac.uk/extra/mokca/ |
| KinMutBase (Ortutay et al., 2005) | Registry of disease-causing mutations in protein kinase domains | http://bioinf.uta.fi/KinMutBase |