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Resource:Babelomics

Name: Resource:Babelomics
Description: An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system .

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.

In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements:

  • Data input: import and quality control for the most common microarray formats
  • Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent).
  • Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis.
  • Genotyping: stratification analysis, association, TDT.
  • Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis.
  • Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis.
Platform: Online tool
Other Name(s): Babelomics 4, Babelomics 4: Gene Expression and Functional Profiling Analysis Suite
Abbreviation: Babelomics
Parent Organization: Resource:CIPF Bioinformatics and Genomics Department
Supporting Agency: Spanish Ministry of Science and Innovation, Red Temtica de Investigacion Cooperativa en Cancer, Instituto de Salud Carlos III
Grant: BIO2008-04212, CEN-2008-1002, RD06/0020/1019
Resource Type(s): Data analysis service
Resource: Resource
URL: http://babelomics.bioinfo.cipf.es
*Id: nif-0000-30144
PMID: PMID 20478823, 18515841, 16845052, 14990455, 15980512, 17478504
Related to: Resource:Gene Ontology Tools, Resource:GO, Resource:BioCarta Pathways, Resource:KEGG, Resource:TRANSFAC, Resource:JASPAR, Resource:OMICtools
Availability: Free for academic use, Account required
Keywords: Platform, Analysis, Transcriptomics, Proteomics, Genomics, Normalization, Clustering, Gene, MiRNA, Protein, Interaction, Text mining, Genotyping, Bioentity, Functional profiling, Statistical analysis, Functional annotation, Regulatory motif, Microarray, FatiGO, Biclustering, NetworkMiner, GEPAS, gene expression
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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Notes

This page uses this default form:Resource

Xref: OMICS_00748

Old URL: http://www.babelomics.org
Alt. URL: http://www.fatigo.org/
Alt. URL: http://www.gepas.org/
Alt. URL: http://babelomics3.bioinfo.cipf.es

Contributors

Aarnaud, Yazin, Zaidaziz



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*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.

Facts about Resource:BabelomicsRDF feed
AbbrevBabelomics  +
AvailabilityFree for academic use  +, and Account required  +
CurationStatuscurated  +
DefiningCitationhttp://babelomics.bioinfo.cipf.es  +
DefinitionAn integrative platform for the analysis o An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system .

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.

In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements:

  • Data input: import and quality control for the most common microarray formats
  • Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent).
  • Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis.
  • Genotyping: stratification analysis, association, TDT.
  • Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis.
  • Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis.

Platform: Online tool unctional analysis.

Platform: Online tool
ExampleImageBabelomics.PNG  +
GrantCategory:BIO2008-04212   +, Category:CEN-2008-1002   +, and Category:RD06/0020/1019   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleData analysis service  +
Idnif-0000-30144  +
Is part ofResource:CIPF Bioinformatics and Genomics Department  +
KeywordsPlatform  +, Analysis  +, Transcriptomics  +, Proteomics  +, Genomics  +, Normalization  +, Clustering  +, Gene  +, MiRNA  +, Protein  +, Interaction  +, Text mining  +, Genotyping  +, Bioentity  +, Functional profiling  +, Statistical analysis  +, Functional annotation  +, Regulatory motif  +, Microarray  +, FatiGO  +, Biclustering  +, NetworkMiner  +, GEPAS  +, and Gene expression  +
LabelResource:Babelomics  +
ModifiedDate27 January 2014  +
PMID20478823, 18515841, 16845052, 14990455, 15980512, 17478504  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToResource:Gene Ontology Tools  +, Resource:GO  +, Resource:BioCarta Pathways  +, Resource:KEGG  +, Resource:TRANSFAC  +, Resource:JASPAR  +, and Resource:OMICtools  +
SuperCategoryResource  +
Supporting AgencySpanish Ministry of Science and Innovation  +, Red Temtica de Investigacion Cooperativa en Cancer  +, and Instituto de Salud Carlos III  +
SynonymBabelomics 4  +, and Babelomics 4: Gene Expression and Functional Profiling Analysis Suite  +