Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments

@article{citeulike:2853945, abstract = {We present a new version of Babelomics, a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available. In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules. Finally, a tool for the de novo' functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org 10.1093/nar/gkn318}, author = {Al-Shahrour, Fatima and Carbonell, Jose and Minguez, Pablo and Goetz, Stefan and Conesa, Ana and Tarraga, Joaquin and Medina, Ignacio and Alloza, Eva and Montaner, David and Dopazo, Joaquin }, citeulike-article-id = {2853945}, doi = {http://dx.doi.org/10.1093/nar/gkn318}, journal = {Nucl. Acids Res.}, keywords = {genomics, proteomics, software, transcriptomics, webserver}, month = {May}, pages = {gkn318+}, posted-at = {2008-06-01 07:02:47}, priority = {2}, title = {Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments}, url = {http://dx.doi.org/10.1093/nar/gkn318}, year = {2008} }

TY - JOUR ID - citeulike:2853945 L3 - citeulike-article-id:2853945 N2 - We present a new version of Babelomics, a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available. In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules. Finally, a tool for the de novo' functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org 10.1093/nar/gkn318 JF - Nucl. Acids Res. TI - Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments SP - gkn318 KW - genomics KW - proteomics KW - software KW - transcriptomics KW - webserver AU - Al-Shahrour, Fatima AU - Carbonell, Jose AU - Minguez, Pablo AU - Goetz, Stefan AU - Conesa, Ana AU - Tarraga, Joaquin AU - Medina, Ignacio AU - Alloza, Eva AU - Montaner, David AU - Dopazo, Joaquin PY - 2008/05/31/ UR - http://dx.doi.org/10.1093/nar/gkn318 ER -