Genomics & Informatics

  • 제5권3호
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  • Pages.133-136
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  • 2007
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  • 1598-866X(pISSN)
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  • 2234-0742(eISSN)
한국유전체학회 (Korea Genome Organization)
권호 표지

GSnet: An Integrated Tool for Gene Set Analysis and Visualization

  • Choi, Yoon-Jeong (Nano Materials Simulation and Fabrication Laboratory, Department of Materials Science and Engineering, KAIST) ;
  • Woo, Hyun-Goo (aboratory of Experimental Carcinogenesis, National Cancer Institute, NIH) ;
  • Yu, Ung-Sik (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)
  • 발행 : 2007.09.30
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초록

The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform. The functional enrichment of a given gene set is calculated using a hypergeometric test based on the Gene Ontology annotation. The protein interaction network is estimated using public data. Set operations allow a complex protein interaction network to be decomposed into a functionally-enriched module of interest. GSnet provides a new framework for gene set analysis by integrating a priori knowledge of a biological network with functional enrichment analysis.

키워드

참고문헌

  1. Alfarano, c., Andrade, C.E., Anthony, K., Bahroos, N., Bajec, M., Bantoft, K., Betel, D., Bobechko, B., Boutilier, K., Burgess, E., Buzadzija, K., Cavero, R, D'Abreo, C., Donaldson, I., Dorairajoo, D., Dumontier, M.J., Dumontier, M.R., Earles, V., Farrall, R, Feldman, H., Garderman, E., Gong, Y., Gonzaga, R, Grytsan, V., Gryz, E., Gu, V., Haldorsen, E., Halupa, A, Haw, R, Hrvojic. A, Hurrell, L., Isserlin, R, Jack, F., Juma, F., Khan, A, Kon, T., Konopinsky, S., Le, V., Lee, E., Ling, S., Magidin, M., Moniakis, J., Montojo, J., Moore, S., Muskat, B., Ng, I., Paraiso, J.P., Parker, B., Pintilie, G., Pirone, R, Salama, J.J., Sgro, S., Shan, T., ShU, Y., Siew, J., Skinner, D., Snyder, K., Stasiuk, R, Strumpf, D., Tuekam, B., Tao, S., Wang, Z., White, M, Willis, R, Wolting, C., Wong, S., Wrong, A, Xin, C., Yao, R, Yates, B., Zhang, S., Zheng, K., Pawson, T., Ouellette, B.F., and Hogue, C.W (2005). The Biornolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res. 33, 0418-0424 https://doi.org/10.1093/nar/gki051
  2. Ashburner, M., Ball, CA, Blake, J.A, Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A, Hill, D.P., Issel-Tarver, L., Kasarskis, A, Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 https://doi.org/10.1038/75556
  3. Bammler, T., Beyer, R.P., Bhattacharya, S., Boorman, G.A, Boyles, A, Bradford, B.U., Bumgarner, RE., Bushel, P.R., Chaturvedi, K., Choi, D., Cunningham, ML., Deng, S., Dressman, H.K., Fannin, R.D., Farin, F.M., Freedman, J.H., Fry, R.C., Harper, A, Humble, M.C., Hurban, P., Kavanagh, T.J., Kaufmann, W.K., Kerr, K.F., Jing, L., Lapidus, J.A, Lasarev, M.R., Li. J., Li, YJ., Lobenhofer, E.K., Lu, X., Malek, R.L., Milton, S., Nagalla, S.R., O'malley, J.P., Palmer, V.S., Pattee, P., Paules, R.S., Perou, C.M., Phillips, K., Qin, L.X., Qiu, Y, Quigley, S.D., Rodland, M., Rusyn, I., Samson, L.D., Schwartz, D.A., Shi, Y., Shin, J.L., Sieber, S.O., Slifer, S., Speer, M.C., Spencer, P.S., Sproles, D.I., Swenberg, J.A., Suk, W.A, Sullivan, R.C., Tian, R, Tennant, R.W, Todd, S.A., Tucker, C.J., Van Houten, B., Weis, S.K., Xuan, S., Zarbl, H. Members of the Toxicogenomics Research Consortium. (2005). Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods 2,351-356 https://doi.org/10.1038/nmeth754
  4. Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Statio Soc. B. 57, 280-300
  5. Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M., and Sherlock, G. (2004). GO::TermFinderopen source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes Bioinformatics 20, 3710-3715 https://doi.org/10.1093/bioinformatics/bth456
  6. Curtis, R.K., Oresic, M., and Vidal-Puig, A (2005). Pathways to the analysis of microarray data. Trends Biotechnol. 23, 429-435 https://doi.org/10.1016/j.tibtech.2005.05.011
  7. Jeong, H., Mason, S.P., Barabasi, A-L., and Oltvai, Z.N. (2001). Lethality and centrality in protein networks. Nature 411,41-42 https://doi.org/10.1038/35075138
  8. Khatri, P. andDraghici, S. (2005). Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21, 3587-3595 https://doi.org/10.1093/bioinformatics/bti565
  9. Lee, H.K., Hsu, A K., Sajdak, J., Qin, J., and Pavlidis, P. (2004). Co-expression analysis of human genes across many microarray data sets. Genome Res. 14, 1085-94 https://doi.org/10.1101/gr.1910904
  10. Nikolsky, Y., Nikolskaya, T., and Bugrim, A (2005). Biological networks and analysis of experimental data in drug discovery. Drug Discov. Today 10,653-662 https://doi.org/10.1016/S1359-6446(05)03420-3
  11. Rhodes, D.R and Chinnaiyan, A.M. (2005).Integrative analysis of the cancer transcriptome. Nat. Genet. 37,S31-S37 https://doi.org/10.1038/ng1570
  12. Shannon, P., Markiel, A, Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504 https://doi.org/10.1101/gr.1239303
  13. Subramanian, A, Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, MA, Paulovich, A, Pomeroy, S.L., Golub, T.R, Lander, E.S., and Mesirov, J.P. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. 102, 15545-15550
  14. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J., andChurch., G.M. (1999). Systematic determination of genetic network architecture. Nat. Genet. 22, 281-285 https://doi.org/10.1038/10343
  15. Wheeler, D.L., Barrett, 1., Benson, DA, Bryant, S.H., Canese, K., Church, D.M., DiCuccio, M., Edgar, R, Federhen, S., Helmberg, w., Kenton, D.L., Khovayko, O., Lipman, D.J., Madden, T.L., Maglott, D.R, Ostell, J., Pontius, J.U., Pruitt, K.D., Schuler, G.D., Schriml, L.M., Sequeira, E., Sherry, S.T., Sirotkin, K., Starchenko, G., Suzek, T.O., Tatusov, R., Tatusova, T.A, Wagner, L., and Yaschenko, E.. (2005). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 33, D39-D45