SBCDDB: Sleeping Beauty Cancer Driver Database for gene discovery in mouse models of human cancers

Nucleic Acids Research

Volumn 46, Issue D1, 2018, Pages D1011-D1017

  Newberg, Justin Y ^a,b   Mann, Karen M ^a,b   Mann, Michael B ^a,b   Jenkins, Nancy A ^a,c   Copeland, Neal G ^a,c  

^a HOUSTON METHODIST RESEARCH INSTITUTE   (United States)

^b H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE DISCOVERY; GENE FREQUENCY; GENETIC DATABASE; GENETIC PROCEDURES; HUMAN; MALIGNANT NEOPLASM; MOUSE; MUTAGENESIS; NONHUMAN; POLYMERASE CHAIN REACTION; POPULATION RESEARCH; PRIORITY JOURNAL; PYROSEQUENCING; RETROPOSON; STATISTICAL ANALYSIS; ANIMAL; DISEASE MODEL; EXPERIMENTAL NEOPLASM; GENE EXPRESSION REGULATION; GENETICS; TRANSPOSON; TUMOR GENE;

ANIMALS; DATABASES, GENETIC; DISEASE MODELS, ANIMAL; DNA TRANSPOSABLE ELEMENTS; GENES, NEOPLASM; MICE; MUTAGENESIS, INSERTIONAL; NEOPLASMS, EXPERIMENTAL;

EID: 85040937474     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx956     Document Type: Article

References (24)

1. Copeland, N.G., Jenkins, N.A. (2010) Harnessing transposons forcancer gene discovery. Nat. Rev. Cancer, 10, 696-706.
2. Mann, K.M., Jenkins, N.A., Copeland, N.G., Mann, M.B. (2014)Transposon insertional mutagenesis models of cancer. Cold SpringHarbor Protoc., 2014, pdb.top069849.
3. Mann, M.B., Jenkins, N.A., Copeland, N.G., Mann, K.M. (2014)Sleeping Beauty mutagenesis: Exploiting forward genetic screens forcancer gene discovery. Curr. Opin. Genet. Dev., 24, 16-22.
4. Akagi, K., Suzuki, T., Stephens, R.M., Jenkins, N.A. andCopeland, N.G. (2004) RTCGD: Retroviral tagged cancer genedatabase. Nucleic Acids Res., 32, D523-D527.
5. Abbott, K.L., Nyre, E.T., Abrahante, J., Ho, Y.-Y., Isaksson Vogel, R.and Starr, T.K. (2015) The Candidate Cancer Gene Database: Adatabase of cancer driver genes from forward genetic screens in mice.Nucleic Acids Research, 43, D844-D848.
6. Tokheim, C.J., Papadopoulos, N., Kinzler, K.W., Vogelstein, B. andKarchin, R. (2016) Evaluating the evaluation of cancer driver genes.Proc. Natl. Acad. Sci. U.S.A., 113, 14330-14335.
7. Cerami, E., Gao, J., Dogrusoz, U., Gross, B.E., Sumer, S.O., Aksoy, B.A., Jacobsen, A., Byrne, C.J., Heuer, M.L., Larsson, E., et al.(2012) The cBio cancer genomics portal: An open platform forexploring multidimensional cancer genomics data. Cancer Discov., 2, 401-404.
8. Gao, J., Aksoy, B.A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S.O., Sun, Y., Jacobsen, A., Sinha, R., Larsson, E., et al. (2013)Integrative analysis of complex cancer genomics and clinical profilesusing the cBioPortal. Sci. Signal., 6, pl1.
9. Zhang, J., Baran, J., Cros, A., Guberman, J.M., Haider, S., Hsu, J., Liang, Y., Rivkin, E., Wang, J., Whitty, B., et al. (2011) InternationalCancer Genome Consortium Data Portal-a one-stop shop forcancer genomics data. Database, 2011, bar026.
10. Grossman, R.L., Heath, A.P., Ferretti, V., Varmus, H.E., Lowy, D.R., Kibbe, W.A., Staudt, L.M. (2016) Toward a shared vision forcancer genomic data.N. Engl. J. Med., 375, 1109-1112.
11. Genovesi, L.A., Ng, C.G., Davis, M.J., Remke, M., Taylor, M.D., Adams, D.J., Rust, A.G., Ward, J.M., Ban, K.H., Jenkins, N.A., et al.(2013) Sleeping Beauty mutagenesis in a mouse medulloblastomamodel defines networks that discriminate between human molecularsubgroups. Proc. Natl. Acad. Sci. U.S.A., 110, E4325-E4334.
12. Rangel, R., Lee, S.-C., Hon-Kim Ban, K., Guzman-Rojas, L., Mann, M.B., Newberg, J.Y., Kodama, T., McNoe, L.A., Selvanesan, L., Ward, J.M., et al. (2016) Transposon mutagenesis identifies genes thatcooperate with mutant Pten in breast cancer progression. Proc. Natl.Acad. Sci. U.S.A., 113, E7749-E7758.
13. March, H.N., Rust, A.G., Wright, N.A., ten Hoeve, J., de Ridder, J., Eldridge, M., van der Weyden, L., Berns, A., Gadiot, J., Uren, A., et al.(2011) Insertional mutagenesis identifies multiple networks ofcooperating genes driving intestinal tumorigenesis. Nat. Genet., 43, 1202-1209.
14. Takeda, H., Wei, Z., Koso, H., Rust, A.G., Yew, C.C.K., Mann, M.B., Ward, J.M., Adams, D.J., Copeland, N.G., Jenkins, N.A. (2015)Transposon mutagenesis identifies genes and evolutionary forcesdriving gastrointestinal tract tumor progression. Nat. Genet., 47, 142-150.
15. Bard-Chapeau, E.A., Nguyen, A.-T., Rust, A.G., Sayadi, A., Lee, P., Chua, B.Q., New, L.-S., de Jong, J., Ward, J.M., Chin, C.K.Y., et al.(2014) Transposon mutagenesis identifies genes driving hepatocellularcarcinoma in a chronic hepatitis B mouse model. Nat. Genet., 46, 24-32.
16. Mann, K.M., Ward, J.M., Yew, C.C.K., Kovochich, A., Dawson, D.W., Black, M.A., Brett, B.T., Sheetz, T.E., Dupuy, A.J., Initiative, A.P.C.G.et al. (2012) Sleeping Beauty mutagenesis reveals cooperatingmutations and pathways in pancreatic adenocarcinoma. Proc. Natl.cad. Sci. U.S.A., 109, 5934-5941.
17. Perez-Mancera, P.A., Rust, A.G., van der Weyden, L., Kristiansen, G., Li, A., Sarver, A.L., Silverstein, K.A.T., Grutzmann, R., Aust, D., Rummele, P., et al. (2012) The deubiquitinase USP9X suppressespancreatic ductal adenocarcinoma. Nature, 486, 266-270.
18. Mann, M.B., Black, M.A., Jones, D.J., Ward, J.M., Yew, C.C.K., Newberg, J.Y., Dupuy, A.J., Rust, A.G., Bosenberg, M.W., McMahon, M., et al. (2015) Transposon mutagenesis identifies geneticdrivers of BrafV600E melanoma. Nat Genet, 47, 486-495.
19. Mann, K.M., Newberg, J.Y., Black, M.A., Jones, D.J., Amaya-Manzanares, F., Guzman-Rojas, L., Kodama, T., Ward, J.M., Rust, A.G., van der Weyden, L., et al. (2016) Analyzing tumorheterogeneity and driver genes in single myeloid leukemia cells withSBCapSeq. Nat. Biotech., 34, 962-972.
20. Takeda, H., Rust, A.G., Ward, J.M., Yew, C.C.K., Jenkins, N.A. andCopeland, N.G. (2016) Sleeping Beauty transposon mutagenesisidentifies genes that cooperate with mutant Smad4 in gastric cancerdevelopment. Proc. Natl. Acad. Sci. U.S.A.s, 113, E2057-E2065.
21. Brett, B.T., Berquam-Vrieze, K.E., Nannapaneni, K., Huang, J., Scheetz, T.E., Dupuy, A.J. (2011) Novel molecular andcomputational methods improve the accuracy of insertion siteanalysis in sleeping beauty-induced tumors. PLOS ONE, 6, e24668.
22. Chen, E.Y., Tan, C.M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G.V., Clark, N.R., Ma'ayan, A. (2013) Enrichr: Interactive andcollaborative HTML5 gene list enrichment analysis tool. BMCBioinformatics, 14, 128-128.
23. Kuleshov, M.V., Jones, M.R., Rouillard, A.D., Fernandez, N.F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S.L., Jagodnik, K.M., Lachmann, A., et al. (2016) Enrichr: A comprehensive gene setenrichment analysis web server 2016 update. Nucleic Acids Res., 44, W90-W97.
24. Bostock, M., Ogievetsky, V., Heer, J. (2011) D3 Data-DrivenDocuments. IEEE Trans. Vis. Comput. Graph., 17, 2301-2309.