Acknowledgements

MAGI was created by the Raphael research group at Brown University.

Funding

MAGI is supported by Brown University, the National Science Foundation and National Institutes of Health.



Data

MAGI uses public mutation data from The Cancer Genome Atlas's Pan-Cancer and stomach cancer projects [1-2],



the HINT, HPRD, iRefIndex, and Multinet interaction networks [3-6],



and the PFAM, SMART, and Conserved Domain protein domain databases [7-10].



MAGI also uses annotations from the Database of Curated Mutations.

References

  1. Wildstein, J. et al. (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113–1120.
  2. The Cancer Genome Atlas Research Network. (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513, 202-209.
  3. Das J. and Yu H. (2012) HINT: High-quality protein interactomes and their applications in understanding human disease. BMC Systems Biology, 30;6(1):92.
  4. Prasad, T. S. K. et al. (2009) Human Protein Reference Database - 2009 Update. Nucleic Acids Research. 37, D767-72.
  5. Razick, S., Magklaras, G., Donaldson, IM. (2008) iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics. 9(1):405.
  6. Khurana E., Fu Y., Chen J., Gerstein, M. (2013) Interpretation of Genomic Variants Using a Unified Biological Network Approach. PLoS Comput Biol 9(3): e1002886.
  7. Punta et al. (2012) The Pfam protein families database. Nucleic Acids Research Database Issue 40:D290-D301
  8. Schultz et al. (1998) SMART, a simple modular architecture research tool: Identification of signaling domains. PNAS 95 (11) 5857-5864.
  9. Letunic, I., Doerks, T., Bork, P. (2012) SMART 7: recent updates to the protein domain annotation resource. Nucl. Acids Res. 40 (D1): D302-D305.
  10. Marchler-Bauer et al. (2013) CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 41(D1):D348-52. Epub.