The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
GSEA-P: a desktop application for Gene Set Enrichment Analysis
Open accessAbstract
Gene Set Enrichment Analysis (GSEA) is a computational method that assesses whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. We report the availability of a new version of the Java based software (GSEA-P 2.0) that represents a major improvement on the previous release through the addition of a leading edge analysis component, seamless integration with the Molecular Signature Database (MSigDB) and an embedded browser that allows users to search for gene sets and map them to a variety of microarray platform formats. This functionality makes it possible for users to directly import gene sets from MSigDB for analysis with GSEA. We have also improved the visualizations in GSEA-P 2.0 and added links to a new form of concise gene set annotations called Gene Set Cards. These additions, as well as other improvements suggested by over 3500 users who have downloaded the software over the past year have been incorporated into this new release of the GSEA-P Java desktop program. Availability: GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.mit.edu/GSEA Contact: mesirov@broad.mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
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) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Self-citationMootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197
Self-citationAn oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis.
Sweet-Cordero, A., Mukherjee, S., Subramanian, A., You, H., Roix, J. J., Ladd-Acosta, C., Mesirov, J., Golub, T. R., & Jacks, T. (2005) · Nature Genetics · doi:10.1038/ng1490 · Cited by 414
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Research works printed but not linked: 3
- Bourquin, 2006, Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling, Proc. Natl Acad. Sci. USA, 103, 3339, 10.1073/pnas.0511150103 · DOI
- Liu, 2003, NetAffx: affymetrix probesets and annotations, Nucleic Acids Res, 31, 82, 10.1093/nar/gkg121 · DOI · Paper page
- Rebhan, 1997, GeneCards: Encyclopedia for Genes, Proteins and Diseases, Weizmann Institute of Science, Bioinformatics Unit and Genome Center, Trends in Genetics, 13, 163, 10.1016/S0168-9525(97)01103-7 · DOI · Paper page
Cited by
The Molecular Signatures Database Hallmark Gene Set Collection
Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015) · Cell Systems · doi:10.1016/j.cels.2015.12.004 · Cited by 13,807
Self-citationEnrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G. V., Clark, N. R., & Ma’ayan, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-128 · Cited by 7,814
Gene set knowledge discovery with enrichr
Xie, Z., Bailey, A., Kuleshov, M. V., Clarke, D. J. B., Evangelista, J. E., Jenkins, S. L., Lachmann, A., Wojciechowicz, M. L., Kropiwnicki, E., Jagodnik, K. M., et al. (2021) · Current Protocols · doi:10.1002/cpz1.90 · Cited by 3,451
The Achilles' heel of senescent cells: from transcriptome to senolytic drugs
Zhu, Y., Tchkonia, T., Pirtskhalava, T., Gower, A. C., Ding, H., Giorgadze, N., Palmer, A. K., Ikeno, Y., Hubbard, G. B., Lenburg, M., et al. (2015) · Aging Cell · doi:10.1111/acel.12344 · Cited by 2,584
“The ranked list was then used to perform a pre-ranked GSEA analysis using the Entrez Gene versions of gene sets obtained from the Molecular Signatures Database (Subramanian et al., 2007).”
MethodReactome: a database of reactions, pathways and biological processes
Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1018 · Cited by 1,751
Metadata
- Authors
- Subramanian, A., Kuehn, H., Gould, J., Tamayo, P., & Mesirov, J. P.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-07-20
- Volume
- 23
- Issue
- 23
- Pages
- 3251-3253
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2134582937
- Cited by
- 1,390
- References
- 3
- FWCI
- 10.66
- Type
- journal article
- Language
- en
- Open access
- bronze
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