The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data
Open accessAbstract
Summary: The CluePedia Cytoscape plugin is a search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data. Genes, proteins and miRNAs can be connected based on in silico and/or experimental information and integrated into a ClueGO network of terms/pathways. Interrelations within each pathway can be investigated, and new potential associations may be revealed through gene/protein/miRNA enrichments. A pathway-like visualization can be created using the Cerebral plugin layout. Combining all these features is essential for data interpretation and the generation of new hypotheses. The CluePedia Cytoscape plugin is user-friendly and has an expressive and intuitive visualization. Availability: http://www.ici.upmc.fr/cluepedia/ and via the Cytoscape plugin manager. The user manual is available at the CluePedia website. Contact: bernhard.mlecnik@crc.jussieu.fr or jerome.galon@crc.jussieu.fr Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara, A., & Griffiths-Jones, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1027 · Cited by 3,634
Reactome: 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
Barsky, A., Gardy, J. L., Hancock, R. E. W., & Munzner, T. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm057 · Cited by 175
Cited by
Mlecnik, B., Bindea, G., Angell, H. K., Maby, P., Angelova, M., Tougeron, D., Church, S. E., Lafontaine, L., Fischer, M., Fredriksen, T., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.02.025 · Cited by 1,034
Self-citationDe Simone, M., Arrigoni, A., Rossetti, G., Gruarin, P., Ranzani, V., Politano, C., Bonnal, R. J. P., Provasi, E., Sarnicola, M. L., Panzeri, I., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.10.021 · Cited by 687
Hepatocytes direct the formation of a pro-metastatic niche in the liver
Lee, J. W., Stone, M. L., Porrett, P. M., Thomas, S. K., Komar, C. A., Li, J. H., Delman, D., Graham, K., Gladney, W. L., Hua, X., et al. (2019) · Nature · doi:10.1038/s41586-019-1004-y · Cited by 402
Microglia Actively remodel adult hippocampal neurogenesis through the phagocytosis secretome
Diaz-Aparicio, I., Paris, I., Sierra-Torre, V., Plaza-Zabala, A., Rodríguez-Iglesias, N., Márquez-Ropero, M., Beccari, S., Huguet, P., Abiega, O., Alberdi, E., et al. (2020) · The Journal of Neuroscience · doi:10.1523/jneurosci.0993-19.2019 · Cited by 333
Van den Eynde, M., Mlecnik, B., Bindea, G., Fredriksen, T., Church, S. E., Lafontaine, L., Haicheur, N., Marliot, F., Angelova, M., Vasaturo, A., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.11.003 · Cited by 281
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Metadata
- Authors
- Bindea, G., Galon, J., & Mlecnik, B.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-01-16
- Volume
- 29
- Issue
- 5
- Pages
- 661-663
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2152026276
- Cited by
- 1,061
- References
- 5
- FWCI
- 15.20
- Type
- journal article
- Language
- en
- Open access
- hybrid
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