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Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

Babelomics is a response to the growing necessity of integrating and analyzing different types of genomic data in an environment that allows an easy functional interpretation of the results. Babelomics includes a complete suite of methods for the analysis of gene expression data that include normali...

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Autores principales: Medina, Ignacio, Carbonell, José, Pulido, Luis, Madeira, Sara C., Goetz, Stefan, Conesa, Ana, Tárraga, Joaquín, Pascual-Montano, Alberto, Nogales-Cadenas, Ruben, Santoyo, Javier, García, Francisco, Marbà, Martina, Montaner, David, Dopazo, Joaquín
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896184/
https://www.ncbi.nlm.nih.gov/pubmed/20478823
http://dx.doi.org/10.1093/nar/gkq388
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author Medina, Ignacio
Carbonell, José
Pulido, Luis
Madeira, Sara C.
Goetz, Stefan
Conesa, Ana
Tárraga, Joaquín
Pascual-Montano, Alberto
Nogales-Cadenas, Ruben
Santoyo, Javier
García, Francisco
Marbà, Martina
Montaner, David
Dopazo, Joaquín
author_facet Medina, Ignacio
Carbonell, José
Pulido, Luis
Madeira, Sara C.
Goetz, Stefan
Conesa, Ana
Tárraga, Joaquín
Pascual-Montano, Alberto
Nogales-Cadenas, Ruben
Santoyo, Javier
García, Francisco
Marbà, Martina
Montaner, David
Dopazo, Joaquín
author_sort Medina, Ignacio
collection PubMed
description Babelomics is a response to the growing necessity of integrating and analyzing different types of genomic data in an environment that allows an easy functional interpretation of the results. Babelomics includes a complete suite of methods for the analysis of gene expression data that include normalization (covering most commercial platforms), pre-processing, differential gene expression (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls and TDTs, and allows population stratification analysis and correction). All these genomic data analysis facilities are integrated and connected to multiple options for the functional interpretation of the experiments. Different methods of functional enrichment or gene set enrichment can be used to understand the functional basis of the experiment analyzed. Many sources of biological information, which include functional (GO, KEGG, Biocarta, Reactome, etc.), regulatory (Transfac, Jaspar, ORegAnno, miRNAs, etc.), text-mining or protein–protein interaction modules can be used for this purpose. Finally a tool for the de novo functional annotation of sequences has been included in the system. This provides support for the functional analysis of non-model species. Mirrors of Babelomics or command line execution of their individual components are now possible. Babelomics is available at http://www.babelomics.org.
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spelling pubmed-28961842010-07-02 Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling Medina, Ignacio Carbonell, José Pulido, Luis Madeira, Sara C. Goetz, Stefan Conesa, Ana Tárraga, Joaquín Pascual-Montano, Alberto Nogales-Cadenas, Ruben Santoyo, Javier García, Francisco Marbà, Martina Montaner, David Dopazo, Joaquín Nucleic Acids Res Articles Babelomics is a response to the growing necessity of integrating and analyzing different types of genomic data in an environment that allows an easy functional interpretation of the results. Babelomics includes a complete suite of methods for the analysis of gene expression data that include normalization (covering most commercial platforms), pre-processing, differential gene expression (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls and TDTs, and allows population stratification analysis and correction). All these genomic data analysis facilities are integrated and connected to multiple options for the functional interpretation of the experiments. Different methods of functional enrichment or gene set enrichment can be used to understand the functional basis of the experiment analyzed. Many sources of biological information, which include functional (GO, KEGG, Biocarta, Reactome, etc.), regulatory (Transfac, Jaspar, ORegAnno, miRNAs, etc.), text-mining or protein–protein interaction modules can be used for this purpose. Finally a tool for the de novo functional annotation of sequences has been included in the system. This provides support for the functional analysis of non-model species. Mirrors of Babelomics or command line execution of their individual components are now possible. Babelomics is available at http://www.babelomics.org. Oxford University Press 2010-07-01 2010-05-16 /pmc/articles/PMC2896184/ /pubmed/20478823 http://dx.doi.org/10.1093/nar/gkq388 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Medina, Ignacio
Carbonell, José
Pulido, Luis
Madeira, Sara C.
Goetz, Stefan
Conesa, Ana
Tárraga, Joaquín
Pascual-Montano, Alberto
Nogales-Cadenas, Ruben
Santoyo, Javier
García, Francisco
Marbà, Martina
Montaner, David
Dopazo, Joaquín
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
title Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
title_full Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
title_fullStr Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
title_full_unstemmed Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
title_short Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
title_sort babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896184/
https://www.ncbi.nlm.nih.gov/pubmed/20478823
http://dx.doi.org/10.1093/nar/gkq388
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