WebGestalt 2017: A more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

Nucleic Acids Research

Volumn 45, Issue W1, 2017, Pages W130-W137

  Wang, Jing ^a   Vasaikar, Suhas ^a   Shi, Zhiao ^a   Greer, Michael ^b   Zhang, Bing ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BOVINE; COMPUTER INTERFACE; GENE; GENETICS; HUMAN; INTERNET; MOUSE; NEOPLASM; RAT; SOFTWARE;

ANIMALS; CATTLE; GENES; HUMANS; INTERNET; MICE; NEOPLASMS; RATS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 85023191744     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkx356     Document Type: Article

References (19)

1. Zhang, B., Kirov, S. and Snoddy, J. (2005) WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res., 33, W741-W748.
2. Wang, J., Duncan, D., Shi, Z. and Zhang, B. (2013) WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res., 41, W77-W83.
3. Khatri, P., Sirota, M. and Butte, A. J. (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput. Biol., 8, e1002375.
4. 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.
5. Wang, J., Qian, J., Hoeksema, M. D., Zou, Y., Espinosa, A. V., Rahman, S. M., Zhang, B. and Massion, P. P. (2013) Integrative genomics analysis identifies candidate drivers at 3q26-29 amplicon in squamous cell carcinoma of the lung. Clin. Cancer Res., 19, 5580-5590.
6. Wang, J., Ma, Z., Carr, S. A., Mertins, P., Zhang, H., Zhang, Z., Chan, D. W., Ellis, M. J., Townsend, R. R., Smith, R. D. et al. (2017) Proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Mol. Cell. Proteomics, 16, 121-134.
7. Kohler, S., Bauer, S., Horn, D. and Robinson, P. N. (2008) Walking the interactome for prioritization of candidate disease genes. Am. J. Hum. Genet., 82, 949-958.
8. Vandin, F., Clay, P., Upfal, E. and Raphael, B. J. (2012) Discovery of mutated subnetworks associated with clinical data in cancer. Pac. Symp. Biocomput., 2012, 55-66.
9. Chatr-Aryamontri, A., Oughtred, R., Boucher, L., Rust, J., Chang, C., Kolas, N. K., O'Donnell, L., Oster, S., Theesfeld, C., Sellam, A. et al. (2017) The BioGRID interaction database: 2017 update. Nucleic Acids Res., 45, D369-D379.
10. Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S. et al. (2016) The Reactome pathway Knowledgebase. Nucleic Acids Res., 44, D481-D487.
11. Mi, H., Poudel, S., Muruganujan, A., Casagrande, J. T. and Thomas, P. D. (2016) PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res., 44, D336-D342.
12. Pinero, J., Bravo, A., Queralt-Rosinach, N., Gutierrez-Sacristan, A., Deu-Pons, J., Centeno, E., Garcia-Garcia, J., Sanz, F. and Furlong, L. I. (2017) DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res., 45, D833-D839.
13. Wishart, D. S., Knox, C., Guo, A. C., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z. and Woolsey, J. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res., 34, D668-D672.
14. Margolin, A. A., Wang, K., Lim, W. K., Kustagi, M., Nemenman, I. and Califano, A. (2006) Reverse engineering cellular networks. Nat. Protoc., 1, 662-671.
15. Shi, Z., Wang, J. and Zhang, B. (2013) NetGestalt: integrating multidimensional omics data over biological networks. Nat. Methods, 10, 597-598.
16. Reimand, J., Arak, T., Adler, P., Kolberg, L., Reisberg, S., Peterson, H. and Vilo, J. (2016) g: Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res., 44, W83-W89.
17. Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A. et al. (2016) Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res., 44, W90-W97.
18. Alonso, R., Salavert, F., Garcia-Garcia, F., Carbonell-Caballero, J., Bleda, M., Garcia-Alonso, L., Sanchis-Juan, A., Perez-Gil, D., Marin-Garcia, P., Sanchez, R. et al. (2015) Babelomics 5. 0: functional interpretation for new generations of genomic data. Nucleic Acids Res., 43, W117-W121.
19. Mitrea, C., Taghavi, Z., Bokanizad, B., Hanoudi, S., Tagett, R., Donato, M., Voichita, C. and Draghici, S. (2013) Methods and approaches in the topology-based analysis of biological pathways. Front. Physiol., 4, 278.