Pathview Web: User friendly pathway visualization and data integration

Nucleic Acids Research

Volumn 45, Issue W1, 2017, Pages W501-W508

  Luo, Weijun ^a,b   Pant, Gaurav ^a,b   Bhavnasi, Yeshvant K ^a,b   Blanchard, Steven G ^a,b   Brouwer, Cory ^a,b  

^a UNIVERSITY OF NORTH CAROLINA AT CHARLOTTE   (United States)

^b University of North Carolina at Charlotte   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER GRAPHICS; COMPUTER INTERFACE; DATA INTEGRATION; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; ONLINE SYSTEM; PATHVIEW WEB SERVER; PRIORITY JOURNAL; PROCESS DEVELOPMENT; WEB BROWSER; WORKFLOW; GENE EXPRESSION; INTERNET; METABOLOMICS; SOFTWARE;

COMPUTER GRAPHICS; GENE EXPRESSION; INTERNET; METABOLOMICS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 85023180870     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx372     Document Type: Article

References (27)

1. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H. and Kanehisa, M. (1999) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 27, 29-34.
2. Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691-D697.
3. Kelder, T., van Iersel, M. P., Hanspers, K., Kutmon, M., Conklin, B. R., Evelo, C. T. and Pico, A. R. (2012) WikiPathways: building research communities on biological pathways. Nucleic Acids Res., 40, D1301-D1307.
4. Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A., Kubo, A. et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., 42, D459-D471.
5. Mi, H., Muruganujan, A. and Thomas, P. D. (2013) PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res., 41, D377-D386.
6. Cerami, E. G., Gross, B. E., Demir, E., Rodchenkov, I., Babur, O., Anwar, N., Schultz, N., Bader, G. D. and Sander, C. (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res., 39, D685-D690.
7. Luo, W., Friedman, M. S., Shedden, K., Hankenson, K. D. and Woolf, P. J. (2009) GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics, 10, 161.
8. Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A., 102, 15545-15550.
9. Tarca, A. L., Draghici, S., Khatri, P., Hassan, S. S., Mittal, P., Kim, J. S., Kim, C. J., Kusanovic, J. P. and Romero, R. (2009) A novel signaling pathway impact analysis. Bioinformatics, 25, 75-82.
10. Luo, W. and Brouwer, C. (2013) Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics, 29, 1830-1831.
11. Hu, Z., Chang, Y. C., Wang, Y., Huang, C. L., Liu, Y., Tian, F., Granger, B. and Delisi, C. (2013) VisANT 4. 0: Integrative network platform to connect genes, drugs, diseases and therapies. Nucleic Acids Res., 41, W225-W231.
12. Kono, N., Arakawa, K., Ogawa, R., Kido, N., Oshita, K., Ikegami, K., Tamaki, S. and Tomita, M. (2009) Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PLoS One, 4, e7710.
13. Kutmon, M., van Iersel, M. P., Bohler, A., Kelder, T., Nunes, N., Pico, A. R. and Evelo, C. T. (2015) PathVisio 3: an extendable pathway analysis toolbox. PLoS Comput. Biol., 11, e1004085.
14. Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L. and Ideker, T. (2011) Cytoscape 2. 8: new features for data integration and network visualization. Bioinformatics, 27, 431-432.
15. Yamada, T., Letunic, I., Okuda, S., Kanehisa, M. and Bork, P. (2011) iPath2. 0: interactive pathway explorer. Nucleic Acids Res., 39, W412-W415.
16. Kramer, F., Bayerlova, M. and Beissbarth, T. (2014) R-based software for the integration of pathway data into bioinformatic algorithms. Biology, 3, 85-100.
17. Villaveces, J. M., Koti, P. and Habermann, B. H. (2015) Tools for visualization and analysis of molecular networks, pathways, and-omics data. Adv. App. Bioinformatics Chem., 8, 11-22.
18. Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L. A., Rhee, S. Y. and Stitt, M. (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J., 37, 914-939.
19. Junker, B. H., Klukas, C. and Schreiber, F. (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7, 109.
20. 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.
21. King, Z. A., Drager, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E. and Palsson, B. O. (2015) Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS Comput. Biol., 11, e1004321.
22. Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. and Morishima, K. (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res., 45, D353-D361.
23. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
24. Kamburov, A., Cavill, R., Ebbels, T. M., Herwig, R. and Keun, H. C. (2011) Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. Bioinformatics, 27, 2917-2918.
25. Xia, J., Sinelnikov, I. V., Han, B. and Wishart, D. S. (2015) MetaboAnalyst 3. 0-making metabolomics more meaningful. Nucleic Acids Res., 43, W251-W257.
26. Luo, W. (2013) Pathview package: a tool set for pathway based data integration and visualization.
27. Emery, L. A., Tripathi, A., King, C., Kavanah, M., Mendez, J., Stone, M. D., de las Morenas, A., Sebastiani, P. and Rosenberg, C. L. (2009) Early dysregulation of cell adhesion and extracellular matrix pathways in breast cancer progression. Am. J. Pathol., 175, 1292-1302.