Coordinated perspectives and enhanced force-directed layout for the analysis of network motifs

Conferences in Research and Practice in Information Technology Series

Volumn 60, Issue , 2006, Pages 39-48

  Klukas, Christian ^a   Schreiber, Falk ^a   Schẅobbermeyer, Henning ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

Coordinated perspectives; Force directed layout; Graph drawing; Information visualisation; Multiple views; Network analysis; Network motifs

Indexed keywords

COORDINATED PERSPECTIVES; FORCE-DIRECTED LAYOUT; GRAPH DRAWING; INFORMATION VISUALISATION; MULTIPLE VIEWS; NETWORK MOTIF;

DRAWING (GRAPHICS); ELECTRIC NETWORK ANALYSIS;

VISUALIZATION;

EID: 84877981954     PISSN: 14451336     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (28)

1. Bachmaier, C., Brandenburg, F. J., Forster, M., Raitner, M. & Holleis, P. (2005), Gravisto: Graph visualization toolkit, in 'Proceedings of the International Symposium on Graph Drawing (GD 2004)', Vol. 3383 of Lecture Notes in Computer Science, Springer, pp. 502-503.
2. Batagelj, V. & Mrvar, A. (2004), Pajek - Analysis and Visualization of Large Networks, in M. J̈unger & P. Mutzel, eds, 'Graph Drawing Software', Springer, pp. 77-103.
3. Battista, G. D., Eades, P., Tamassia, R. & Tollis, I. G. (1999), Graph Drawing: Algorithms for the Visualization of Graphs, Prentice-Hall.
4. Conant, G. C. & Wagner, A. (2003), 'Convergent evolution of gene circuits', Nature Genetices 34(3), 264-266.
5. Dobrin, R., Beg, Q. K., Barab́asi, A.-L. & Oltvai, Z. N. (2004), 'Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network', BMC Bioinformatics 5(1), 10.
6. Figure 16: Cluster layout for frequency concept F2. In contrast to Figure 15 lower cluster-forces have been used.
7. Eades, P. (1984), 'A heuristic for graph drawing', Congressus Numerantium 42, 149-160.
8. Eades, P. & Huang, M. L. (2000), 'Navigating clustered graphs using force-directed methods.', Journal of Graph Algorithms Applications 4(3), 157-181.
9. Fruchterman, T. & Reingold, E. (1991), 'Graph drawing by force-directed placement', Software - Practice and Experience 21(11), 1129-1164.
10. Garey, M. R. & Johnson, D. S. (1979), Computers and Intractability: A Guide to the Theory of NP-Completeness, W.H. Freeman and Company, New York.
11. Harary, F. & Palmer, E. M. (1973), Graphical Enumeration, Academic Press, New York.
12. Himsolt, M. (2000), 'Graphlet: design and implementation of a graph editor', Software - Practice and Experience 30(11), 1303-1324.
13. Kashtan, N., Itzkovitz, S., Milo, R. & Alon, U. (2002), Mfinder tool guide, Technical report, Department of Molecular Cell Biology and Computer Science & Applied Mathematics, Weizman Institute of Science.
14. Klukas, C., Koscḧutzki, D. & Schreiber, F. (2005), 'Graph pattern analysis with PatternGravisto', Journal of Graph Algorithms and Applications 9(1), 19-29.
15. Kuramochi, M. & Karypis, G. (2004), Finding frequent patterns in a large sparse graph, in 'SIAM International Conference on Data Mining (SDM- 04)'.
16. Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., Zeitlinger, J., Jennings, E. G., Murray, H. L., Gordon, D. B., Ren, B., Wyrick, J. J., Tagne, J. B., Volkert, T. L., Fraenkel, E., Gifford, D. K. & Young, R. A. (2002), 'Transcriptional regulatory networks in Saccharomyces cerevisiae', Science 298(5594), 799-804.
17. Mangan, S. & Alon, U. (2003), 'Structure and function of the feed-forward loop network motif', Proceedings of the National Academy of Sciences 100(21), 11980-11985.
18. Mangan, S., Zaslaver, A. & Alon, U. (2003), 'The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks', Journal of Molecular Biology 334(2), 197-204.
19. Maslov, S. & Sneppen, K. (2002), 'Specificity and stability in topology of protein networks', Science 296, 910-913.
20. Maslov, S., Sneppen, K. & Alon, U. (2003), Correlation profiles and motifs in complex networks, in S. Bornholdt & H. G. Schuster, eds, 'Handbook of Graphs and Networks: From the Genome to the Internet', Wiley-VCH, Berlin, pp. 168-198.
21. Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. & Alon, U. (2002), 'Network motifs: Simple building blocks of complex networks', Science 298(5594), 824-827.
22. Schreiber, F. & Schẅobbermeyer, H. (2004), Towards motif detection in networks: Frequency concepts and flexible search, in 'Proceedings of the International Workshop on Network Tools and Applications in Biology (NETTAB'04)', pp. 91-102.
23. Schreiber, F. & Schẅobbermeyer, H. (2005), 'MAVisto: A tool for the exploration of network motifs', Bioinformatics 21(17), 3572-3574.
24. Shen-Orr, S., Milo, R., Mangan, S. & Alon, U. (2002), 'Network motifs in the transcriptional regulation network of Escherichia coli', Nature Genetics 31(1), 64-68.
25. Sporns, O. & K̈otter, R. (2004), 'Motifs in brain networks', PLoS Biology 2(11), e369.
26. Vanetik, N., Gudes, E. & Shimony, E. (2002), Computing frequent graph patterns from semistructured data, in 'Proceedings of the IEEE International Conference on Data Mining (ICDM)', pp. 458-465.
27. Wuchty, S., Oltvai, Z. N. & Barab́asi, A.-L. (2003), 'Evolutionary conservation of motif constituents in the yeast protein interaction network', Nature Genetics 35(1), 176-179.
28. Zhang, L. V., King, O. D., Wong, S. L., Goldberg, D. S., Tong, A. H., Lesage, G., Andrews, B., Bussey, H., Boone, C. & Rot, F. P. (2005), 'Motifs, themes and thematic maps of an integrated saccharomyces cerevisiae interaction network', Journal of Biology 4(2), Epub.