Babelomics statistics

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Citations per year

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Tool usage distribution map

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Associated diseases

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Popular tool citations

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

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


No version available

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 citations

 (416)
library_books

Ehrlichia chaffeensis TRP75 Interacts with Host Cell Targets Involved in Homeostasis, Cytoskeleton Organization, and Apoptosis Regulation To Promote Infection

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

[…] uenced, 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 in the human […]

call_split

Combining targeted panel based resequencing and copy number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies

2018
Sci Rep
PMCID: 5869593
PMID: 29588463
DOI: 10.1038/s41598-018-23520-1
call_split See protocol

[…] .nih.gov/variation/tools/1000genomes/), 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, Po […]

library_books

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

2018
PLoS One
PMCID: 5844516
PMID: 29522525
DOI: 10.1371/journal.pone.0190184

[…] In the common QTL regions 729 genes were identified, and 180 genes on the backcross-specific regions. To focus in a more affordable candidate gene list, criteria based on functionality, examined with Fatigo and VarElect tools, and gene expression differences from parallel RNA-Seq studies (divergent pigs for the analyzed traits) [,] were used to prioritize them. A total of 85 candidate genes were s […]

library_books

Strong phenotypic plasticity limits potential for evolutionary responses to climate change

2018
Nat Commun
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] 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 anno […]

library_books

Genome wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle

2018
BMC Genomics
PMCID: 5812220
PMID: 29439661
DOI: 10.1186/s12864-018-4523-2

[…] cess” (14%), “cellular process” (12%) and “localization” (11%). The search for GO terms and/or KEGG pathways overrepresented on the gene set identified vs those present in whole bovine gene set using FatiGO method [] did not produce significant results (data not shown).Fig. 5 […]

library_books

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo and autopolyploidization events

2018
BMC Biol
PMCID: 5785856
PMID: 29370802
DOI: 10.1186/s12915-018-0482-y

[…] red to the olive proteome using one-to-one and one-to-many orthologs. GO term enrichment of proteins duplicated at the different species-specific expansions and duplication peaks was calculated using FatiGO []. […]


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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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