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UNIT 15.2 Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome

  1. Belinda M. Giardine,
  2. Cathy Riemer,
  3. Richard Burhans,
  4. Aakrosh Ratan,
  5. Webb Miller

Published Online: 1 SEP 2012

DOI: 10.1002/0471250953.bi1502s39

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Giardine, B. M., Riemer, C., Burhans, R., Ratan, A. and Miller, W. 2012. Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome. Current Protocols in Bioinformatics. 39:15.2:15.2.1–15.2.27.

Author Information

  1. Pennsylvania State University, University Park, Pennsylvania

Publication History

  1. Published Online: 1 SEP 2012

Literature Cited

  1. Literature Cited
  2. Internet Resources
  3. Supplementary File
  • Adzhubei, I.A., Schmidt, S., Peshkin, L., Ramensky, V.E., Gerasimova, A., Bork, P., Kondrashov, A.S., and Sunyaev, S.R. 2010. A method and server for predicting damaging missense mutations. Nat. Methods 7:248-249.
  • Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., and Taylor, J. 2010. Galaxy: A web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 89:19.10.1-19.10.21.
  • Davis, A.P., Murphy, C.G., Saraceni-Richards, C.A., Rosenstein, M.C., Wiegers, T.C., and Mattingly, C.J. 2009. Comparative Toxicogenomics Database: A knowledgebase and discovery tool for chemical.gene.disease networks. Nucleic Acids Res. 37:D786-D792.
  • Drmanac, R., Sparks, A.B., Callow, J.M., Halpern, A.L., Burns, N.L., Kermani, B.G., Carnevali, P., Nazarenko, I., Nilsen, G.B., Yeung, G, Dahl, F., Fernandez, A., Staker, B., Pant, K.P., Baccash, J., Borcherding, A.P., Brownley, A., Cedeno, R., Chen, L., Chernikoff, D., Cheung, A., Chirita, R., Curson, B., Ebert, J.C., Hacker, C.R., Hartlage, R., Hauser, B., Huang, S., Jiang, Y., Karpinchyk, V., Koenig, M., Kong, C., Landers, T., Le, C., Liu, J., McBride, C.E., Morenzoni, M., Morey, R.E., Mutch, K., Perazich, H., Perry, K., Peters, B.A., Peterson, J., Pethiyagoda, C.L., Pothuraju, K., Richter, C., Rosenbaum, A.M., Roy, S., Shafto, J., Sharanhovich, U., Shannon, K.W., Sheppy, C.G., Sun, M., Thakuria, J.V., Tran, A., Vu, D., Zaranek, A.W., Wu, X., Drmanac, S., Oliphant, A.R., Banyai, W.C., Martin, B., Ballinger, D.G., Church, G.M., and Reid, C.A. 2009. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327:78-81.
  • Ferretti, V., Poitras, C., Bergeron, D., Coulombe, B., Robert, F., and Blanchette, M. 2007. PReMod: A database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res. 35:D122-D126.
  • Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W.J., and Nekrutenko, A. 2005. Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15:1451-1455.
  • Giardine, B., Riemer, C., Hefferon, T., Thomas, D., Hsu, F., Zielenski, J., Sang, Y., Elnitski, L., Cutting, G., Trumbower, H., Kern, A., Kuhn, R., Patrinos, G.P., Hughes, J., Higgs, D., Chui, D., Scriver, C., Phommarinh, M., Patnaik, S.K., Blumenfeld, O., Gottlieb, B., Vihinen, M., Väliaho, J., Kent, J., Miller, W., and Hardison, R.C. 2007. PhenCode: Connecting ENCODE data with mutations and phenotype. Hum. Mutat. 28:554-562.
  • Goecks, J., Nekrutenko, A., Taylor, J.; Galaxy Team. 2010. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11:R86.
  • Huang, D.W., Sherman, B.T., and Lempicki, R.A. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4:44-57.
  • Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D., and Kent, W.J. 2004. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32:D493-D496.
  • Kumar, P., Henikoff, S., and Ng, P.C. 2009. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4:1073-1081.
  • Reimand, J., Kull, M., Peterson, H., Hansen, J., and Vilo, J. 2007. g:Profiler: A web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 35:W193-W200.
  • Seal, R.L., Gordon, S.M., Lush, M.J., Wright, M.W., and Bruford, E.A. 2011. genenames.org: The HGNC resources in 2011. Nucleic Acids Res. 39:D514-519.
  • Siepel, A., Pollard, K.S., and Haussler, D. 2006. New methods for detecting lineage-specific selection. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205, Venice, Italy.
  • Taylor, J., Tyekucheva, S., King, D.C., Hardison, R.C., Miller, W., and Chiaromonte, F. 2006. ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res. 16:1596-1604.

Internet Resources

  1. Literature Cited
  2. Internet Resources
  3. Supplementary File

The main public instance of Galaxy.

A collection of human phenotype-associated SNPs from Locus-Specific Databases.

A version of this tutorial in HTML format.

Descriptions of file formats used by the UCSC Table Browser.

Supplementary File

  1. Literature Cited
  2. Internet Resources
  3. Supplementary File

This is an alternate URL to access the file “test.masterVar.gz” cited in Basic Protocol 1, Necessary Resources, Files on page 15.2.3.