Babelomics protocols

Babelomics specifications

Information


Unique identifier OMICS_00748
Name Babelomics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 5.0
Stability Stable
Registration required Yes
Maintained Yes

Subtool


  • SNOW

Versioning


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Maintainer


  • person_outline Joaquín Dopazo <>

Information


Unique identifier OMICS_00748
Name Babelomics
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 5.0
Stability Stable
Maintained Yes

Subtool


  • SNOW

Maintainer


  • person_outline Joaquín Dopazo <>

Publications for Babelomics

Babelomics IN pipelines

 (5)
2017
PMCID: 5483458
PMID: 28694818
DOI: 10.3389/fpls.2017.01113

[…] in a set of differentially expressed genes respect to a reference group composed of all genes in the microarray with an arabidopsis thaliana homolog was carried out using the program fatigo+ (babelomics, http://babelomics.bioinfo.cipf.es) (ballester et al., 2011). a fisher two-tailed test (p-value < 0.05) was independently performed for gene ontology analysis of induced and repressed […]

2017
PMCID: 5483458
PMID: 28694818
DOI: 10.3389/fpls.2017.01113

[…] differentially expressed genes respect to a reference group composed of all genes in the microarray with an arabidopsis thaliana homolog was carried out using the program fatigo+ (babelomics, http://babelomics.bioinfo.cipf.es) (ballester et al., 2011). a fisher two-tailed test (p-value < 0.05) was independently performed for gene ontology analysis of induced and repressed genes., special […]

2011
PMCID: 3129315
PMID: 21635778
DOI: 10.1186/1471-213X-11-32

[…] wing shape in comparison to the control line, for each sex separately, to look for blocks of functionally related genes with similar phenotypic effects across the list. both programmes belong to the babelomics suite of bioinformatic tools which is available online [71]. they both distribute the genes among the terms corresponding to each category in a non-exclusive manner (that is, a given gene […]

2010
PMCID: 2806919
PMID: 20090954
DOI: 10.1371/journal.pone.0008729

[…] and at each time point, we produced venn diagrams at venny website (http://bioinfogp.cnb.csic.es/tools/venny/index.html). for functional profiling of selected genes, we employed fatigo (http://www.babelomics.org/), which is a web-based functional analysis tool to determine whether any given cluster of genes has an enriched biologically relevant term, when compared to other gene clusters [77], […]

2010
PMCID: 2951363
PMID: 20949061
DOI: 10.1371/journal.pone.0013213

[…] deposited in the gene expression omnibus repository as series number gse20190 (www.ncbi.nlm.nih.gov/geo/)., an analysis was performed using fatigo (a web-based program for functional profiling; www.babelomics.org) to indentify functional enrichment by comparing the two lists of differentially regulated genes from endometrium and blood by means of a fisher's exact test [54]. furthermore, pathway […]

Babelomics institution(s)
Computational Genomics Department, Centro de Investigacio n Principe Felipe (CIPF), Valencia, Spain; Computational Genomics Chair, Bull-CIPF, Valencia, , Spain; Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain; Department of Medicine, University of Cambridge, School of Clinical Medicine, Addenbrooke’s Hospital, Cambridge, UK; Fundacion Investigacion Clinico de Valencia - INCLIVA, Valencia, Spain; Functional Genomics Node, (INB) at CIPF, Valencia, Spain; HPC Services, University of Cambridge, Cambridge, UK
Babelomics funding source(s)
Supported by Spanish Ministry of Economy and Competitiveness [BIO2011-27069], Conselleria d’Educacio of the Valencian Community [PROMETEOII/2014/025]; EU FP7-PEOPLE Project MLPM [316861]; Fundacio la Marato TV3 [151/C/2013].

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