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IBM Journal of Research and Development

Systems Biology   Volume 50, Number 6, 2006
Table of contents: HTMLPDF This article: HTMLPDF   Copyright info

Visualization of complementary systems biology data with parallel heatmaps - References

by R. M. Podowski,
B. Miller,
and W. W. Wasserman
References

  1. B. R. Zeeberg, W. Feng, G. Wang, M. D. Wang, A. T. Fojo, M. Sunshine, S. Narasimhan, D. W. Kane, W. C. Reinhold, S. Lababidi, K. J. Bussey, J. Riss, J. C. Barrett, and J. N. Weinstein, “GoMiner: A Resource for Biological Interpretation of Genomic and Proteomic Data,” Genome Biol. 4, No. 4 (2003); see http://genomebiology.com/2003/4/4/R28.
  2. D. A. Hosack, G. Dennis, Jr., B. T. Sherman, H. C. Lane, and R. A. Lempicki, “Identifying Biological Themes Within Lists of Genes with EASE,” Genome Biol. 4, No. 10 (2003); see http://genomebiology.com/2003/4/10/R70.
  3. M. D. Robinson, J. Grigull, N. Mohammad, and T. R. Hughes, “FunSpec: A Web-Based Cluster Interpreter for Yeast,” BMC Bioinformat. 3, No. 1, 35 (2002).
  4. L. R. Matthews, P. Vaglio, J. Reboul, H. Ge, B. P. Davis, J. Garrels, S. Vincent, and M. Vidal, “Identification of Potential Interaction Networks Using Sequence-Based Searches for Conserved Protein–Protein Interactions or ‘Interologs,' ”, Genome Res. 11, No. 12, 2120–2126 (2001).
  5. J. M. Stuart, E. Segal, D. Koller, and S. K. Kim, “A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules,” Science 302, No. 5643, 249–255 (2003).
  6. V. van Noort, B. Snel, and M. A. Huynen, “Predicting Gene Function by Conserved Co-Expression,” Trends Genet. 19, No. 5, 238–242 (2003).
  7. R. D. Meyer and D. Cook, “Visualization of Data,” Current Opin. Biotechnol. 11, No. 1, 89–96 (2000).
  8. IEEE Computer Society; see http://www.computer.org/portal/site/ieeecs/index.jsp.
  9. Association for Computing Machinery; see http://www.acm.org.
  10. N. Boukhelifa and P. J. Rodgers, “A Model and Software System for Coordinated and Multiple Views in Exploratory Visualization,” Info. Visualiz. 2, No. 4, 258–269 (2003).
  11. Proceedings of the 2nd International Conference on Coordinated and Multiple Views in Exploratory Visualization, London, England (2004); see http://csdl.computer.org/comp/proceedings/cmv/2004/2179/00/2179toc.htm.
  12. P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker, “Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks,” Genome Res. 13, No. 11, 2498–2504 (2003).
  13. B.-J. Breitkreutz, C. Stark, and M. Tyers, “Osprey: A Network Visualization System,” Genome Biol. 4, No. 3, R22 (2003).
  14. E. Altermann and T. R. Klaenhammer, “PathwayVoyager: Pathway Mapping Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Database,” BMC Genom. 6, No. 1, 60 (2005).
  15. KEGG: Kyoto Encyclopedia of Genes and Genomes; see http://www.genome.jp/kegg/.
  16. Reactome, Cold Spring Harbor Laboratory, European Bioinformatics Institute, and GO Consortium; see http://www.reactome.org.
  17. M. B. Eisen, P. T. Spellman, P. O. Brown, and D. Botstein, “Cluster Analysis and Display of Genome-Wide Expression Patterns,” Proc. Natl. Acad. Sci. USA 95, No. 25, 14863–14868 (1998).
  18. A. P. Gasch, M. Huang, S. Metzner, D. Botstein, S. J. Elledge, and P. O. Brown, “Genomic Expression Responses to DNA-Damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p,” Molec. Biol. Cell 12, No. 10, 2987–3003 (2001).
  19. J. N. Weinstein, T. G. Myers, P. M. O'Connor, S. H. Friend, A. J. Fornace, Jr., K. W. Kohn, T. Fojo, S. E. Bates, L. V. Rubinstein, N. L. Anderson, J. K. Buolamwini, W. W. van Osdol, A. P. Monks, D. A. Scudiero, E. A. Sausville, D. W. Zaharevitz, B. Bunow, V. N. Viswanadhan, G. S. Johnson, R. E. Wittes, and K. D. Paull, “An Information-Intensive Approach to the Molecular Pharmacology of Cancer,” Science 275, No. 5298, 343–349 (1997).
  20. X. Wen, S. Fuhrman, G. S. Michaels, D. B. Carr, S. Smith, J. L. Baker, and R. Somogyi, “Large-Scale Temporal Gene Expression Mapping of Central Nervous System Development,” Proc. Natl. Acad. Sci. USA 95, No. 1, 334–339 (1998).
  21. Hierarchical Clustering Explorer, Human–Computer Interaction Laboratory, University of Maryland; see http://www.cs.umd.edu/hcil/hce/index.html.
  22. J. Seo and B. Shneiderman, “Interactively Exploring Hierarchical Clustering Results,” IEEE Computer 35, No. 7, 80–86 (2002).
  23. R. Edgar, M. Domrachev, and A. E. Lash, “Gene Expression Omnibus: NCBI Gene Expression and Hybridization Array Data Repository,” Nucl. Acids Res. 30, No. 1, 207–210 (2002).
  24. W. Wu and W. S. Noble, “Genomic Data Visualization on the Web,” Bioinformatics 20, No. 11, 1804–1805 (2004).
  25. I. M. Dresen, J. Hüsing, E. Kruse, T. Boes, and K.-H. Jöckel, “Software Packages for Quantitative Microarray-Based Gene Expression Analysis,” Current Pharmaceut. Biotechnol. 4, 417–437 (2003).
  26. M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock, “Gene Ontology: Tool for the Unification of Biology,” Nature Genet. 25, 25–29 (2000).
  27. S. G. Lee, W. S. Lee, and Y. S. Kim, “GOODIES: GO Based Data Mining Tool for Characteristic Attribute Interpretation on a Group of Biological Entities,” Genome Informat. 14, 675–676 (2003).
  28. K. Nishimura, K. Abe, S. Ishikawa, S. Tsutsumi, K. Hirota, H. Aburatani, and M. Hirose, “A PCA Based Method of Gene Expression Visual Analysis,” Genome Informat. 14, 346–347 (2003).
  29. E. Segal, B. Taskar, A. Gasch, N. Friedman, and D. Koller, “Rich Probabilistic Models for Gene Expression,” Bioinformatics 17, S 243–S 252 (2001).
  30. G. S. Davidson, B. Hendrickson, D. K. Johnson, C. E. Meyers, and B. N. Wylie, “Knowledge Mining With VxInsight: Discovery Through Interaction,” J. Intell. Info. Syst. 11, No. 3, 259–285 (1998).
  31. D. Keim and H.-P. Kriegel, “VisDB: Database Exploration Using Multidimensional Visualization,” IEEE Computer Graph. & Appl. 14, No. 5, 40–49 (1994).
  32. P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein, and B. Futcher, “Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces Cerevisiae by Microarray Hybridization,” Molec. Biol. Cell 9, No. 12, 3273–3297 (1998).
  33. Ö. Johansson, W. Alkema, W. W. Wasserman, and J. Lagergren, “Identification of Functional Clusters of Transcription Factor Binding Motifs in Genome Sequences: The MSCAN Algorithm,” Bioinformatics 19, Supplement 1, I169–I176 (2003).
  34. A. Sandelin, A. Höglund, B. Lenhard, and W. W. Wasserman, “Integrated Analysis of Yeast Regulatory Sequences for Biologically Linked Clusters of Genes,” Funct. & Integrat. Genom. 3, No. 3, 125–134 (2003).
  35. SOURCE, Genetics Department, Stanford University; see http://source.stanford.edu/cgi-bin/source/sourceSearch.
  36. GO Term Finder; see http://db.yeastgenome.org/cgi-bin/GO/goTermFinder.
  37. T. I. Lee, N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber, N. M. Hannett, C. T. Harbison, C. M. Thompson, I. Simon, J. Zeitlinger, E. G. Jennings, H. L. Murray, D. B. Gordon, B. Ren, J. J. Wyrick, J.-B. Tagne, T. L. Volkert, E. Fraenkel, D. K. Gifford, and R. A. Young, “Transcriptional Regulatory Networks in Saccharomyces Cerevisiae,Science 298, No. 5594, 799–804 (2002).
  38. Saccharomyces Genome Database; see http://www.yeastgenome.org/.
  39. S. Aerts, P. Van Loo, Y. Moreau, and B. DeMoor, “A Genetic Algorithm for the Detection of New Cis-Regulatory Modules in Sets of Coregulated Genes,” Bioinformatics 20, No. 12, 1974–1976 (2004).
  40. oPOSSUM; see http://cisreg.ca/cgi-bin/oPOSSUM/opossum.
  41. G. Getz, E. Levine, E. Domany, and M. Q. Zhang, “Super-Paramagnetic Clustering of Yeast Gene Expression Profiles,” Physica A 279, 457–464 (2000).
  42. Parallel HeatMap Viewer Project; see http://www.cisreg.ca/raf/PHM/.
  43. GenePilot, TG Services, Inc.; see http://genepilot.com.


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