The Pathway Tools cellular overview diagram and Omics Viewer

Nucleic Acids Research

Volumn 34, Issue 13, 2006, Pages 3771-3778

  Paley, Suzanne M ^a   Karp, Peter D ^a  

^a SRI INTERNATIONAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; PERIPLASMIC PROTEIN;

AUTOMATION; BIOCHEMISTRY; CELL METABOLISM; CELL STRUCTURE; CELL TRANSPORT; COMPUTER PROGRAM; CYTOLOGY; GENE EXPRESSION; GENETIC DATABASE; HUMAN; IMAGE ANALYSIS; IMAGE ENHANCEMENT; INFORMATION PROCESSING; INTERNET; METABOLITE; METABOLOMICS; NONHUMAN; PATTERN RECOGNITION; PRIORITY JOURNAL; PUBLICATION; REACTION ANALYSIS; REVIEW; SEMANTICS; SIGNAL TRANSDUCTION; VISUAL SYSTEM; ARTICLE; BIOLOGICAL MODEL; COMPUTER GRAPHICS; COMPUTER INTERFACE; ESCHERICHIA COLI; FACTUAL DATABASE; METABOLISM; PROTEOMICS;

COMPUTER GRAPHICS; DATABASES, FACTUAL; DATABASES, GENETIC; ESCHERICHIA COLI; GENE EXPRESSION; INTERNET; METABOLISM; MODELS, BIOLOGICAL; PROTEOMICS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33748745026     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl334     Document Type: Review

References (14)

1. Karp,P.D., Paley,S. and Romero,P. (2002) The Pathway Tools Software. Bioinformatics, 18, S225-S232.
2. Karp,P.D., Ouzounis,C.A., Moore-Kochlacs,C., Goldovsky,L., Kaipa,P., Ahren,D., Tsoka,S., Darzentas,N., Kunin,V. and Lopez-Bigas,N. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res., 33, 6083-6089.
3. Karp,P., Krummenacker,M., Paley,S. and Wagg,J. (1999) Integrated pathway/ genome databases and their role in drug discovery. Trend. Biotechnol., 17, 275-281.
4. Saraiya,P., North,C. and Duca,K. (2005) Visualizing biological pathways: requirements analysis, systems evaluation and research agenda. Inform. Visualiz., 4, 191-205.
5. Michal,G. (1982) Biochemical Pathways Wall Chart. Boehringer Mannheim GmbH Biochemica.
6. Tusher,V.G., Tibshirani,R. and Chu,G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci., USA, 98, 5116-5121.
7. Chang,D.E., Smalley,D.J., Tucker,D.L., Leatham,M.P., Norris,W.E., Stevenson,S.J., Anderson,A.B., Grissom,J.E., Laux,D.C., Cohen,P.S. et al. (2004) Carbon nutrition of Escherichia coli in the mouse intestine. Proc. Natl Acad. Sci., USA, 101, 7427-7432.
8. Nikiforova,V.J., Kopka,J., Tolstikov,V., Fiehn,O., Hopkins,L., Hawkesford,M.J., Hesse,H. and Hoefgen,R. (2005) Systems rebalancing of metabolism in response to sulfur deprivation, as revealed by metabolome analysis of Arabidopsis plants. Plant Physiol., 138, 304-318.
9. Kanehisa,M., Goto,S., Kawashima,S., Okuno,Y. and Hattori,M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, D277-D280.
10. Arakawa,K., Kono,N., Yamada,Y., Mori,H. and Tomita,M. (2005) KEGG-based pathway visualization tool for complex omics data. In Silico Biol., 5, 419-423.
11. Joshi-Tope,G., Gillespie,M., Vastrik,I., D'Eustachio,P., Schmidt,E., de Bono,B., Jassal,B., Gopinath,G.R., Wu,G.R., Matthews,L. et al. (2005) Reactome: A knowledge base of biological pathways. Nucleic Acids Res., 33, D428-D432.
12. Dahlquist,K.D., Salomonis,N., Vranizan,K., Lawlor,S.C. and Conklin,B.R. (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genet., 31, 19-20.
13. Holford,M., Li,N., Nadkarni,P. and Zhao,H. (2004) VitaPad: Visualization tools for the analysis of pathway data. Bioinformatics, 15, 1596-1602.
14. Chung,H.J., Kim,M., Park,C.H., Kim,J. and Kim,J.H. (2004) ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res., 32, W460-W464.