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Protocols

GO.db specifications

Information


Unique identifier OMICS_22608
Name GO.db
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Version 3.6.0
Requirements
AnnotationDbi, methods, DBI, R(>=2.7.0), AnnotationDbi(>=1.41.4)
Maintained Yes

Documentation


GO.db citations

 (61)
library_books

Gene level differential analysis at transcript level resolution

2018
Genome Biol
PMCID: 5896116
PMID: 29650040
DOI: 10.1186/s13059-018-1419-z

[…] gene list, thresholded at FDR < 0.05, was inputted into a classical GO analysis to test for GO enrichment. topGO_2.26.0 [] was invoked to perform Fisher’s exact test, using gene ontologies drawn from GO.db_3.4.0 and mouse gene annotations drawn from org.Mm.eg.db_3.4.0 []. Furthermore, the gene p values from each aggregation method were used in a GO perturbation test. In the GO perturbation test, g […]

call_split

Gene expression profiling in a mouse model of retinal vein occlusion induced by laser treatment reveals a predominant inflammatory and tissue damage response

2018
PLoS One
PMCID: 5846732
PMID: 29529099
DOI: 10.1371/journal.pone.0191338
call_split See protocol

[…] on between samples, empirical Bayes shrinkage for dispersion estimation and for fold-change estimation, and correction for multiple testing. Gene ontology analysis was done with debrowser 1.2.4.2 and GO.db 3.4.0. The data are available under the accession number GSE101398 at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101398. […]

library_books

An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)

2017
BMC Genet
PMCID: 5741957
PMID: 29273003
DOI: 10.1186/s12863-017-0584-5

[…] onfigured using default values provided by BLAST2GO for all enriched GO terms (adjusted p-value <0.05). Mapping was performed to associate the blast HSP-hits to functionally enriched information from GO DB. All annotations are associated to an evidence code which provides information about the quality of this functional assignment. Default parameters were used to assign Interpro-domain and GO term […]

library_books

Temporally distinct transcriptional regulation of myocyte dedifferentiation and Myofiber growth during muscle regeneration

2017
BMC Genomics
PMCID: 5680785
PMID: 29121865
DOI: 10.1186/s12864-017-4236-y

[…] d for comparisons of log-scaled gene set expression (i.e. enrichment) data between different time points (unpaired, q-value <0.1). Gene sets were defined using annotations obtained from GAGE v2.22.0, go.db v3.2.2, and kegg.db v3.2.2. The R package “pathview” v.1.12.0 and KEGGGraph v1.30.0 were used to visualize gene set expression data in the context of functional pathways [, ].CummeRbund was used […]

library_books

The combinatorial control of alternative splicing in C. elegans

2017
PLoS Genet
PMCID: 5697891
PMID: 29121637
DOI: 10.1371/journal.pgen.1007033

[…] d the gene set with the specific GO term or its child terms. The final values presented for the control set was taken from the total of 1000 randomized samples. All GO annotations were taken from the GO.db (v.3.0.0) and org.Ce.eg.db (v.3.0.0) packages in R. […]

library_books

Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (Vitis vinifera cv. Shiraz)

2017
Front Plant Sci
PMCID: 5670326
PMID: 29163587
DOI: 10.3389/fpls.2017.01860

[…] to as DMGs. DMGs in each pairwise regional comparison were grouped into those showing hypermethylation or hypomethylation, and were next used separately for GO terms enrichment, using the R packages: GO.db () and annotate (). Significant GO terms were selected based on Bonferroni adjusted P-values at significance threshold of 0.05. Finally, GO terms containing DMGs in all three pairwise comparison […]

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