Using process diagrams for the graphical representation of biological networks

Nature Biotechnology

Volumn 23, Issue 8, 2005, Pages 961-966

  Kitano, Hiroaki ^a,b,c,d   Funahashi, Akira ^a,c   Matsuoka, Yukiko ^a,c   Oda, Kanae ^a,d  

^a Systems Biology Institute   (Japan)

^b SONY COMPUTER SCIENCE LABORATORIES INC   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d KEIO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE; GENES; GRAPHIC METHODS; INFORMATION ANALYSIS; PROTEINS;

BIOLOGICAL NETWORKS; GENE REGULATORY NETWORKS; MACHINE-READABLE FORMS; PROTEIN-PROTEIN INTERACTION NETWORKS;

BIOTECHNOLOGY;

BIOLOGY; COMPREHENSION; COMPUTER PROGRAM; GENE CONTROL; INFORMATION PROCESSING; LANGUAGE; MATHEMATICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROCESS MODEL; PROCESS TECHNOLOGY; PROTEIN PROTEIN INTERACTION; REVIEW;

ANIMALS; COMPUTER GRAPHICS; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; HUMANS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 23444439817     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt1111     Document Type: Review

References (14)

1. Hucka, M. et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531
2. Kohn, K.W. Molecular interaction maps as information organizers and simulation guides. Chaos 11, 84-97 (2001).
3. Kohn, K.W. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol. Biol. Cell 10, 2703-2734 (1999).
4. Maimon, R. & Browning, S. in Proceedings of the Second International Conference on Systems Biology (ed. Kitano, H.) 311-7 (Omnipress, Madison, WI, 2001).
5. Pirson, I. et al. The visual display of regulatory information and networks. Trends Cell Biol. 10, 404-408 (2000).
6. Cook, D.L., Farley, J.F. & Tapscott, S.J. A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems. Genome Biol. 2, RESEARCH0012 (2001).
7. Kitano, H. A graphical notation for biochemical networks. Biosilico 1, 169-176 (2003).
8. Aladjem, M.I. et al. Molecular interaction maps-a diagrammatic graphical language for bioregulatory networks. Sci. STKE 2004, pe8 (2004).
9. Maimon, R. & Browning, S. in Proceedings of the Second International Conference on Systems Biology (Pasadena, California, November 5-7, 2001). (Eds. Yi, T.-M., Hucka, M., Morohashi, M., & Kitano, H.) 311-317 (California Institute of Technology, Pasadena, 2001)
10. Funahashi, A., Tanimura, N., Morohashi, M. & Kitano, H. Cell Designer: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO, 1-159-162, (2003).
11. Oda, K. et al. Molecular interaction map of a macrophage. AfCS Research Reports 2, 1-12 (2004).
12. Oda, K., Matsuoka, Y., Funahashi, A. & Kitano, H. A comprehensive pathway map of epidermal growth factor receptor signaling. Molecular Systems Biology, msb4100014-E1-E17 (2005).
13. Kitano, H. et al. Metabolic syndrome and robustness tradeoffs. Diabetes 53 (suppl. 3), S6-S15 (2004).
14. Mi, H. et al. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 33 (Database Issue), D284-288 (2005).