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32 Kirov et al.9. OBO_Team, Open Biomedical Ontologies Foundry. (http://obofoundry.org/).10. Ren, B., Robert, F., Wyrick, J. J., et al. (2000) Genome-wide location and functionof DNA binding proteins. Science 290(5500), 2306–2309.11. Iyer, V. R., Horak, C. E., Scafe, C. S., Bostein, D., Synder, M., and Brown, P. O.(2001) Genomic binding sites of the yeast cell-cycle transcription factors SBFand MBF. Nature 409(6819), 533–538.12. Dorschner, M. O., Hawrylycz, M., Humbert, R., et al. (2004) High-throughputlocalization of functional elements by quantitative chromatin profiling. Nat.Methods. 1(3), 219–225.13. Crawford, G. E., Holt, I. E., Whittle, J., et al. (2006) Genome-wide mapping ofDNase hypersensitive sites using massively parallel signature sequencing(MPSS). Genome Res. 16(1), 123–131.14. Zhang, B., Kirov, S., and Snoddy, J. (2005) WebGestalt: an integrated system forexploring gene sets in various biological contexts. Nucleic Acids Res. 33,W741–W748.15. Zhang, B., Kirov, S., and Snoddy, J. (2005) WebGestalt: an integrated system forexploring gene sets in various biological contexts. Nucleic Acids Res. 33(WebServer issue), W741–W748.16. Zapala, M. A., Hovatta, I., Ellison, J. A., et al. (2005) Adult mouse brain geneexpression patterns bear an embryologic imprint. Proc. Natl. Acad. Sci. USA102(29), 10,357–10,362.17. Maglott, D., Ostell, J., Pruitt, K. D., and Tatusova, T. (2005) Entrez Gene: genecenteredinformation at NCBI. Nucleic Acids Res. 33(Database issue), D54–D58.18. Kasprzyk, A., Keefe, D., Smedley, D., et al. (2004) EnsMart: a generic system forfast and flexible access to biological data. Genome Res. 14(1), 160–169.19. Kirov, S. A., Peng, X., Baker, E., Schmoyer, D., Zhang, B., and Snoddy, J. (2005)GeneKeyDB: a lightweight, gene-centric, relational database to support data miningenvironments. BMC Bioinformatics 6(1), 72.20. Yusuf, D., Lim, J. S., and Wasserman, W. W. (2005) The Gene Set Builder: collation,curation, and distribution of sets of genes. BMC Bioinformatics 6, 305.21. Kirov, S. A., Peng, X., Baker, E., Schmoyer, D., Zhang, B., and Snoddy, J. (2005)GeneKeyDB: A lightweight, gene-centric, relational database to support datamining environments. BMC Bioinformatics 6.22. Beissbarth, T. and Speed, T. P. (2004) GOstat: find statistically overrepresentedGene Ontologies within a group of genes. Bioinformatics 20(9), 1464–1465.23. Shah, N. H. and Fedoroff, N. V. (2004) CLENCH: a program for calculatingCluster ENriCHment using the Gene Ontology. Bioinformatics 20(7), 1196–1197.24. Martin, D., Brun, C., Remy, E., Mouren, O., Thiaffry, D., and Jacq, B. (2004)GOToolBox: functional analysis of gene data sets based on Gene Ontology.Genome Biol. 5(12), R101.25. Dennis, G., Jr., Sherman, B. T., Hosack, D. A., et al. (2003) DAVID: Database forAnnotation, Visualization, and Integrated Discovery. Genome Biol. 4(5), P3.26. Zeeberg, B. R., Feng, W., Wang, G., et al. (2003) GoMiner: a resource for biologicalinterpretation of genomic and proteomic data. Genome Biol. 4(4), R28.
- Page 38: 6 BidautTable 2Folder Layout to Use
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- Page 74: 24 Kirov et al.1. Retrieve the gene
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- Page 82: 28 Kirov et al.Fig. 2. Pathway anal
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- Page 100: 38 Wang and Ochs1. Download the LS-
- Page 104: 40 Wang and OchsFig. 1. The PattRun
- Page 108: 42 Wang and OchsFig. 3. The PattRun
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32 Kirov et al.9. OBO_Team, Open Biomedical Ontologies Foundry. (http://obofoundry.org/).10. Ren, B., Robert, F., Wyrick, J. J., et al. (2000) Genome-wide location and functionof DNA binding proteins. Science 290(5500), 2306–2309.11. Iyer, V. R., Horak, C. E., Scafe, C. S., Bostein, D., Synder, M., and Brown, P. O.(2001) Genomic binding sites of the yeast cell-cycle transcription factors SBFand MBF. Nature 409(6819), 533–538.12. Dorschner, M. O., Hawrylycz, M., Humbert, R., et al. (2004) High-throughputlocalization of functional elements by quantitative chromatin profiling. Nat.Methods. 1(3), 219–225.13. Crawford, G. E., Holt, I. E., Whittle, J., et al. (2006) Genome-wide mapping ofDNase hypersensitive sites using massively parallel signature sequencing(MPSS). Genome Res. 16(1), 123–131.14. Zhang, B., Kirov, S., and Snoddy, J. (2005) WebGestalt: an integrated system forexploring gene sets in various biological contexts. Nucleic Acids Res. 33,W741–W748.15. Zhang, B., Kirov, S., and Snoddy, J. (2005) WebGestalt: an integrated system forexploring gene sets in various biological contexts. Nucleic Acids Res. 33(WebServer issue), W741–W748.16. Zapala, M. A., Hovatta, I., Ellison, J. A., et al. (2005) Adult mouse brain geneexpression patterns bear an embryologic imprint. Proc. Natl. Acad. Sci. USA102(29), 10,357–10,362.17. Maglott, D., Ostell, J., Pruitt, K. D., and Tatusova, T. (2005) Entrez Gene: genecenteredinformation at NCBI. Nucleic Acids Res. 33(Database issue), D54–D58.18. Kasprzyk, A., Keefe, D., Smedley, D., et al. (2004) EnsMart: a generic system forfast and flexible access to biological data. Genome Res. 14(1), 160–169.19. Kirov, S. A., Peng, X., Baker, E., Schmoyer, D., Zhang, B., and Snoddy, J. (2005)GeneKeyDB: a lightweight, gene-centric, relational database to support data miningenvironments. BMC Bioinformatics 6(1), 72.20. Yusuf, D., Lim, J. S., and Wasserman, W. W. (2005) The Gene Set Builder: collation,curation, and distribution of sets of genes. BMC Bioinformatics 6, 305.21. Kirov, S. A., Peng, X., Baker, E., Schmoyer, D., Zhang, B., and Snoddy, J. (2005)GeneKeyDB: A lightweight, gene-centric, relational database to support datamining environments. BMC Bioinformatics 6.22. Beissbarth, T. and Speed, T. P. (2004) GOstat: find statistically overrepresentedGene Ontologies within a group of genes. Bioinformatics 20(9), 1464–1465.23. Shah, N. H. and Fedoroff, N. V. (2004) CLENCH: a program for calculatingCluster ENriCHment using the Gene Ontology. Bioinformatics 20(7), 1196–1197.24. Martin, D., Brun, C., Remy, E., Mouren, O., Thiaffry, D., and Jacq, B. (2004)GOToolBox: functional analysis of gene data sets based on Gene Ontology.Genome Biol. 5(12), R101.25. Dennis, G., Jr., Sherman, B. T., Hosack, D. A., et al. (2003) DAVID: Database forAnnotation, Visualization, and Integrated Discovery. Genome Biol. 4(5), P3.26. Zeeberg, B. R., Feng, W., Wang, G., et al. (2003) GoMiner: a resource for biologicalinterpretation of genomic and proteomic data. Genome Biol. 4(4), R28.