The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
FunRich: An open access standalone functional enrichment and interaction network analysis tool
Abstract
As high‐throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user‐friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed to be used by biologists with minimal or no support from computational and database experts. Using FunRich, users can perform functional enrichment analysis on background databases that are integrated from heterogeneous genomic and proteomic resources (>1.5 million annotations). Besides default human specific FunRich database, users can download data from the UniProt database, which currently supports 20 different taxonomies against which enrichment analysis can be performed. Moreover, the users can build their own custom databases and perform the enrichment analysis irrespective of organism. In addition to proteomics datasets, the custom database allows for the tool to be used for genomics, lipidomics and metabolomics datasets. Thus, FunRich allows for complete database customization and thereby permits for the tool to be exploited as a skeleton for enrichment analysis irrespective of the data type or organism used. FunRich (http://www.funrich.org) is user‐friendly and provides graphical representation (Venn, pie charts, bar graphs, column, heatmap and doughnuts) of the data with customizable font, scale and color (publication quality).
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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108
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Saito, R., Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P.-L., Lotia, S., Pico, A. R., Bader, G. D., & Ideker, T. (2012) · Nature Methods · doi:10.1038/nmeth.2212 · Cited by 1,500
Real-time single-molecule observation of rolling-circle DNA replication
Tanner, N. A., Loparo, J. J., Hamdan, S. M., Jergic, S., Dixon, N. E., & van Oijen, A. M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp006 · Cited by 1,279
The model organism as a system: integrating 'omics' data sets
Joyce, A. R., & Palsson, B. Ø. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1857 · Cited by 785
Visualization of omics data for systems biology
Gehlenborg, N., O'Donoghue, S. I., Baliga, N. S., Goesmann, A., Hibbs, M. A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1436 · Cited by 620
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Khatri, P., Voichiţa, C., Kattan, K. A., Ansari, N., Khatri, A., Georgescu, C., Tarca, A. L., & Drăghici, S. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm327 · Cited by 96
Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data
van den Berg, B. H. J., Thanthiriwatte, C., Manda, P., et al. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-s11-s9 · Cited by 34
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Metadata
- Authors
- Pathan, M., Keerthikumar, S., Ang, C., Gangoda, L., Quek, C. Y. J., Williamson, N. A., Mouradov, D., Sieber, O. M., Simpson, R. J., Salim, A., Bacic, A., Hill, A. F., Stroud, D. A., Ryan, M. T., Agbinya, J. I., Mariadason, J. M., Burgess, A. W., & Mathivanan, S.
- Venue
- PROTEOMICS
- Publisher
- Wiley
- Published
- 2015-06-17
- Volume
- 15
- Issue
- 15
- Pages
- 2597-2601
- ISSN
- 1615-9853 (ISSN-L)
- 1615-9861
- OpenAlex
- W1797058518
- Cited by
- 1,316
- References
- 8
- FWCI
- 34.48
- Type
- journal article
- Language
- en
- Open access
- closed
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- Pathan, M., Keerthikumar, S., Ang, C., Gangoda, L., Quek, C. Y. J., Williamson, N. A., Mouradov, D., Sieber, O. M., Simpson, R. J., Salim, A., Bacic, A., Hill, A. F., Stroud, D. A., Ryan, M. T., Agbinya, J. I., Mariadason, J. M., Burgess, A. W., & Mathivanan, S. (2015). FunRich: An open access standalone functional enrichment and interaction network analysis tool. PROTEOMICS. https://doi.org/10.1002/pmic.201400515
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