GOToolBox protocols

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GOToolBox specifications

Information


Unique identifier OMICS_04140
Name GOToolBox
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Stable
Maintained Yes

Publication for GOToolBox

GOToolBox in pipelines

 (4)
2017
PMCID: 5601981
PMID: 28955347
DOI: 10.3389/fpls.2017.01530

[…] included in further analyses., bli-1 differentially expressed genes were compared to indicated gene sets using virtualplant 1.3 (katari et al., ). for go term analysis we used the online resource gotoolbox (http://genome.crg.es/gotoolbox/), using hypergeometric test with benjamini-hochberg correction for statistical analysis and p-value determination. for goslim analysis we used the online […]

2015
PMCID: 4399909
PMID: 25880195
DOI: 10.1371/journal.ppat.1004692

[…] using tophat version 1.4.0. differential expression between two datasets was analyzed with the genomatix analysis suite (using deseq 1.0.6). gene ontology enrichment was analyzed using gotoolbox [], with a hypergeometric test with benjamini & hochberg correction. level 2 go terms are shown in , and level 3 go terms in fold enrichment is the ratio of the go term frequency […]

2014
PMCID: 4352135
PMID: 25517099
DOI: 10.1038/nature14021

[…] go molecular function, kegg pathway, and interpro protein domains. the benjamini test for multiple hypothesis testing was applied to p values. up- and downregulated genes were also submitted to gotoolbox to perform a hypergeometric test using the benjamini-hochberg correction. enriched go terms were submitted to revigo to remove redundant terms. co-occurrence between our datasets […]

2012
PMCID: 3492862
PMID: 23150795
DOI: 10.7554/eLife.00011.026

[…] ontology (go) analysis; 302 genes had a nascent-seq/rna-seq ratio below 2 sd and 463 genes had a ratio over 2 sd. 13595 genes were considered for this analysis. go analysis has been performed using gotoolbox () (http://genome.crg.es/gotoolbox/), using an hypergeometric test with benjamini-hochberg correction. the background model consisted of the entire list of genes., only genes […]


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GOToolBox in publications

 (56)
PMCID: 5936064
PMID: 29661797
DOI: 10.1242/bio.033944

[…] (five chips per condition). data were analysed using the bioconductor package in r and raw data deposited in gene expression omnibus (geo) (gse111300). gene ontology analysis was performed using gotoolbox (http://genome.crg.es/gotoolbox/). the e11.5 tip microarray data have been previously published () and the raw data are available at geo (gse75860)., mtec cultures in transwell inserts […]

PMCID: 5826290
PMID: 29481322
DOI: 10.7554/eLife.32341.029

[…] (). sequences for major clusters showing enrichment for a given cell type were then analysed using meme-chip ()., potentially regulated genes, with a peak height of at least 10 rpm were submitted to gotoolbox () for go analysis. go term enrichments (frequency in data set divided by expected frequency) were calculated for each cell type., gatc fragments were identified with at least a 10 rpm […]

PMCID: 5601981
PMID: 28955347
DOI: 10.3389/fpls.2017.01530

[…] included in further analyses., bli-1 differentially expressed genes were compared to indicated gene sets using virtualplant 1.3 (katari et al., ). for go term analysis we used the online resource gotoolbox (http://genome.crg.es/gotoolbox/), using hypergeometric test with benjamini-hochberg correction for statistical analysis and p-value determination. for goslim analysis we used the online […]

PMCID: 5770757
PMID: 28776581
DOI: 10.1038/npp.2017.167

[…] (yielding 80 features; ) were selected based on the criteria of the basespace tool and assessed for enrichment in biological themes using the david functional annotation clustering tool, adgo, and gotoolbox, in which the default feature listings and algorithm settings were used., we first performed a meta-analysis of postmortem studies regarding brain ph in patients with schizophrenia […]

PMCID: 5117235
PMID: 27585883
DOI: 10.1242/dmm.026773

[…] false discovery rate (benjamini–hochberg) procedure. for the go analysis, only differentially-expressed genes with an adjusted edger p-value ≤0.001 were included. the go analysis was performed using gotoolbox (http://genome.crg.es/gotoolbox) with enriched categories selected from a hypergeometric test based on a benjamini–hochberg-corrected p-value threshold of 0.05. revigo […]


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GOToolBox institution(s)
Laboratoire de Génétique et Physiologie du Développement, IBDM, CNRS/INSERM/Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France

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