QuickGO protocols

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QuickGO specifications

Information


Unique identifier OMICS_02276
Name QuickGO
Interface Web user interface
Restrictions to use None
Programming languages Javascript
License Apache License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Publication for QuickGO

QuickGO in pipelines

 (14)
2017
PMCID: 5575525
PMID: 28557017
DOI: 10.1111/mmi.13719

[…] was ≤ 0.05 (false‐discovery rate of 5%). differentially expressed genes (degs) were grouped by biological function according to their designated gene ontology (go) terms obtained from the embl‐ebi quickgo database (https://www.ebi.ac.uk/quickgo/). bar charts summarizing the data were generated in graphpad prism version 5.0 (san diego, ca, usa) and heatmaps of gene expression patterns […]

2017
PMCID: 5648782
PMID: 29051502
DOI: 10.1038/s41598-017-13176-8

[…] of conserved signalling pathways as well as key developmental genes. a list of d. melanogaster genes from flybase according to the signalling pathways and developmental processes as assigned by quickgo (http://www.ebi.ac.uk/quickgo/, assessed february 2016) was used as a query to identify homologous sequences in the i. elegans transcriptome. the developmental pathways included embryonic […]

2017
PMCID: 5697066
PMID: 29157281
DOI: 10.1186/s13071-017-2519-4

[…] of the identified proteins was based on gene ontology molecular function, biological process, and cellular component information available from the uniprotkb database (http://www.uniprot.org/) and quickgo (http://www.ebi.ac.uk/quickgo/)., we used signalp 4.1 server to predict the presence and location of signal peptide cleavage sites in amino acid sequences in identified proteins of h. […]

2017
PMCID: 5704591
PMID: 29179763
DOI: 10.1186/s12915-017-0450-y

[…] genes were screened for the corresponding identifiers, the identifiers were assigned to higher level go-terms, and genes were sorted into groups of molecular function and biological process using quickgo [, ]. in gene subsets of particular importance (e.g., 50 most abundant transcripts per cell type), we re-checked the contained gene products without annotation by using the blastp algorithm […]

2016
PMCID: 4928332
PMID: 27357215
DOI: 10.1186/s13071-016-1643-x

[…] peptide and protein levels., to better understand the biological functions of the identified proteins, go annotation was performed based on blast results using the toxodb (http://toxodb.org/toxo/), quickgo (http://www.ebi.ac.uk/quickgo) and david v. 6.7 (http://david.abcc.ncifcrf.gov) databases [–]., to further verify the cags components present in the serum, coronin protein (tgcor) […]


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QuickGO in publications

 (155)
PMCID: 5869700
PMID: 29588496
DOI: 10.1038/s41598-018-23667-x

[…] analysis software. detailed information about the gene included in each category was obtained using quick go, which is a fast browser for gene ontology terms and annotation (http://www.ebi.ac.uk/quickgo/gterm?id=go:0006954#term=annotation). verification of the annotation of the transcripts was performed with blast search (https://blast.ncbi.nlm.nih.gov/blast.cgi), multiple sequence alignment […]

PMCID: 5915032
PMID: 29455577
DOI: 10.1080/15548627.2017.1415189

[…] and cellular locations. table 1.experimental data described by vicinanza et al []. were selected for annotation as they describe the role and location of 8 autophagy-related human proteins. the quickgo [,] filter option was used to retrieve all manual experimental annotations associated with this paper. gene symbol, hgnc gene symbol; go identifier, gene ontology unique numerical identifier; […]

PMCID: 5813370
PMID: 29444698
DOI: 10.1186/s13326-018-0175-z

[…] relationships between classes including classification (is a) and partonomy (part of). this graph structure is commonly used to group genes annotated with related terms in user-facing tools such as quickgo [] and amigo [] and to generate gene sets for enrichment (over- representation) analyses [] to interpret the results of genomics experiments. for example, an experiment to assess […]

PMCID: 5821137
PMID: 29440116
DOI: 10.1161/CIRCGEN.117.001813

[…] go annotations are available from the uniprot go annotation and goc sites (https://www.ebi.ac.uk/goa/downloads, http://www.geneontology.org/gene-associations/) and searchable in the amigo2 and quickgo browsers; go terms are downloadable from the goc site (http://www.geneontology.org/ontology/) and searchable in amigo2 and quickgo. the annotations have also been incorporated into many […]

PMCID: 5874766
PMID: 29385081
DOI: 10.3390/proteomes6010007

[…] of the collective functional categories is the next desirable step. here, various options are available—with potential for deployment in the galaxy platform. for single go terms of interest, the quickgo browser [] enables the user to view the full term definition, as well as to browse closely related terms. for large lists of go terms, the ‘reduce and visualize gene ontology’ (revigo) tool […]


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QuickGO institution(s)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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