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BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments
Open accessAbstract
We present Babelomics, a complete suite of web tools for the functional analysis of groups of genes in high-throughput experiments, which includes the use of information on Gene Ontology terms, interpro motifs, KEGG pathways, Swiss-Prot keywords, analysis of predicted transcription factor binding sites, chromosomal positions and presence in tissues with determined histological characteristics, through five integrated modules: FatiGO (fast assignment and transference of information), FatiWise, transcription factor association test, GenomeGO and tissues mining tool, respectively. Additionally, another module, FatiScan, provides a new procedure that integrates biological information in combination with experimental results in order to find groups of genes with modest but coordinate significant differential behaviour. FatiScan is highly sensitive and is capable of finding significant asymmetries in the distribution of genes of common function across a list of ordered genes even if these asymmetries were not extreme. The strong multiple-testing nature of the contrasts made by the tools is taken into account. All the tools are integrated in the gene expression analysis package GEPAS. Babelomics is the natural evolution of our tool FatiGO (which analysed almost 22,000 experiments during the last year) to include more sources on information and new modes of using it. Babelomics can be found at http://www.babelomics.org.
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The control of the false discovery rate in multiple testing under dependency
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Cited by
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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Reimand, J., Kull, M., Peterson, H., Hansen, J., & Vilo, J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm226 · Cited by 1,545
Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus.
Kobasa, D., Jones, S. M., Shinya, K., Kash, J. C., Copps, J., Ebihara, H., Hatta, Y., Hyun Kim, J., Halfmann, P., Hatta, M., et al. (2007) · Nature · doi:10.1038/nature05495 · Cited by 934
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Differential gene expression analysis of iodide-treated rat thyroid follicular cell line PCCl3
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Metadata
- Authors
- Al-Shahrour, F., Minguez, P., Vaquerizas, J. M., Conde, L., & Dopazo, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-07-01
- Volume
- 33
- Issue
- Web Server
- Pages
- W460-W464
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2120568877
- Cited by
- 254
- References
- 2
- FWCI
- 11.98
- Type
- journal article
- Language
- en
- Open access
- gold
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