Babelomics protocols

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chevron_left Differential expression Gene expression clustering Gene set enrichment analysis Protein-protein interaction prediction Differential expression detection Gene expression classification Driver mutation prioritization Normalization Variant detection Normalization Over-representation analysis Bioinformatics workflows chevron_right
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Babelomics specifications

Information


Unique identifier OMICS_00748
Name Babelomics
Software type Toolkit/Suite
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

Subtools


  • FatiGO
  • FatiScan
  • 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

Subtools


  • FatiGO
  • FatiScan
  • SNOW

Maintainer


  • person_outline Joaquín Dopazo <>

Publications for Babelomics

Babelomics in pipelines

 (19)
2018
PMCID: 5909120
PMID: 29643078
DOI: 10.1128/mSphere.00147-18

[…] and sequenced, and the sequences were analyzed using the genbank database., after sequence analysis, 90 different interacting human proteins were identified (see  in the supplemental material). the babelomics fatigo tool (version 5; http://babelomics.bioinfo.cipf.es) was used to perform a functional ontology analysis of the 90 identified trp75-interacting targets (, ). proteins were classified […]

2017
PMCID: 5216375
PMID: 28059169
DOI: 10.1038/srep40066

[…] annotation were directly retrieved from the ‘gff’ file downloaded at peanutbase website (http://peanutbase.org). go enrichment analysis for degs was performed using fatigo software available at babelomics5 (http://babelomics.org). the enriched go terms were visualized using revigo. the peanut protein sequences were compared with the protein sequences of m. truncatula (mt4.0v1) and l. […]

2015
PMCID: 4652339
PMID: 26581444
DOI: 10.1186/s12864-015-2196-7

[…] the operating procedures of the whole experimental process were detailedly described in our previous study []. for microarray data analysis, the image (cel) files were imported into the online tool babelomics 4.3 (http://babelomics.bioinfo.cipf.es/) []. subsequently, data normalization was performed using rma methods, and expression differentiation analysis was conducted using limma methods. […]

2015
PMCID: 4685628
PMID: 26690675
DOI: 10.1186/s12920-015-0160-7

[…] (fig. ). among all these interactions, we focused on those more likely to be related to the disease, according to their functionalities and gene expression patterns. the application of the david and babelomics [] tools resulted in several gene clusters, one of them composed of 10 genes associated with thyroid gland. according to the cvv values obtained by mdr analyses, only five of those 10 […]

2014
PMCID: 4045674
PMID: 24897521
DOI: 10.1371/journal.pone.0098404

[…] with in-house scripts. all datasets have been deposited to geo (accession number gse51428)., for functional enrichment analysis of the differentially expressed genes (degs) the module fatigo of the babelomics bioinformatics suite and the david functional annotation tools were used. both algorithms use fischer's exact test to check for significant over-representation of gene ontology (go) […]


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Babelomics in publications

 (229)
PMCID: 5933750
PMID: 29723239
DOI: 10.1371/journal.pone.0196666

[…] []. functional protein association networks were identified by using string 10.5 (https://string-db.org/) []. cellular kegg pathway enrichments were determined by using babelomics 4.3 (http://v4.babelomics.org/) []., to validate the binding of candidate mirna on predicted target genes, the human embryonic kidney 293t cell line (hek293t, atcc® crl-1573™) was used. […]

PMCID: 5869593
PMID: 29588463
DOI: 10.1038/s41598-018-23520-1

[…] exome variant server (evs) (http://evs.gs.washington.edu/evs/), exac browser (http://exac.broadinstitute.org/), and ciberer spanish variant server (http://csvs.babelomics.org/); iv) missense snv and in-frame deletions that induced an alteration in the protein predicted as pathogenic in at least 2 of the in silico tools used to predict pathogenicity (sift, […]

PMCID: 5844516
PMID: 29522525
DOI: 10.1371/journal.pone.0190184

[…] the porcine ensembl database, sscrofa11.1. in order to identify potential candidate genes the function of genes within each of the selected regions (±1mb) were examined using varelect [], string [] babelomics [] and ncbi databases (growth, muscle development and fat metabolism related genes). moreover, additional information of gene expression data from a previous study in bc_ld [] […]

PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] to the wet season, i.e. genes with positive and negative fold change values being wet and dry season-biased, respectively., we performed gene ontology (go) gene set enrichment (gse) analyses in babelomics v. 5, using the fatiscan module. as input, we used lists of genes (and their fold change) that were significantly season-biased in thorax, abdomen or both body parts, and the argot2 go […]

PMCID: 5814428
PMID: 29449612
DOI: 10.1038/s41598-018-21439-1

[…] affymetrix® expression console™ software (v1.1). after rma normalization of raw data from 3 biological repeats using the affymetrix algorithm, the normalized data were analyzed using the web-suite babelomics (v4.3). statistical analyses to identify differentially expressed genes (degs) used the limma (linear models for microarray data) test. the fdr (false discovery rate) was used to correct […]


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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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