GOseq statistics

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Protocols

GOseq specifications

Information


Unique identifier OMICS_26373
Name GOseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 1.32.0
Stability Stable
Requirements
AnnotationDbi, stats, graphics, BiocGenerics, utils, rtracklayer, edgeR, R(>=2.11.0), BiasedUrn, GO.db, org.Hs.eg.db, mgcv, geneLenDataBase(>=1.9.2)
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Alicia Oshlack

Publication for GOseq

GOseq citations

 (264)
call_split

The extent of liver injury determines hepatocyte fate toward senescence or cancer

2018
PMCID: 5951829
PMID: 29760381
DOI: 10.1038/s41419-018-0622-x
call_split See protocol

[…] and “complete” method for analyzing different genes based on the same gene ontology (i.e., “regulation of cell proliferation”, “cell cycle” or “aging”) or “hepatocellular carcinoma” marker genes. The GOseq R package was used to perform GO enrichment analysis of different cluster genes. A corrected P-value < 0.05 was adopted as the standard for judging statistically significant enrichment of cluste […]

library_books

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose utilizing derivatives 8b and 2032

2018
Biotechnol Biofuels
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x

[…] gy (GO) associations were extracted from the results of InterProScan with translated plasmid ORF sequences. Cluster-based enrichment test with sets of responsive genes (FDR < 0.05) was performed with goseq package [] from Bioconductor (http://bioconductor.org), the two gene-level statistics summarization tests—Fisher’s combined probability test [] and summarization of median gene-level fold change […]

call_split

The plant hormone abscisic acid regulates the growth and metabolism of endophytic fungus Aspergillus nidulans

2018
Sci Rep
PMCID: 5916901
PMID: 29695775
DOI: 10.1038/s41598-018-24770-9
call_split See protocol

[…] ). P-values were adjusted by the Benjamini & Hochberg’s method. DEGs were selected with an adjusted P-value < 0.05. Functional classification of DEGs was performed by GO enrichment analysis using the GOseq R package with corrected P-value < 0.05. Enrichment of DEGs in the KEGG metabolic pathways was analyzed by the KOBAS software. Transcriptional changes in abundance (P-value < 0.05) were used to […]

call_split

Community Development between Porphyromonas gingivalis and Candida albicans Mediated by InlJ and Als3

2018
MBio
PMCID: 5915736
PMID: 29691333
DOI: 10.1128/mBio.00202-18
call_split See protocol

[…] P. gingivalis genes were annotated with their associated Gene Ontology identifiers from UniProt (http://www.uniprot.org/). GO enrichment/overrepresentation analysis was performed by the use of the R GOSeq package, which implements a Wallenius hypergeometric distribution to account for bias based on gene length. Protein interaction networks were drawn from significantly differentially expressed ge […]

call_split

Effect of early calf hood nutrition on the transcriptomic profile of subcutaneous adipose tissue in Holstein Friesian bulls

2018
BMC Genomics
PMCID: 5916831
PMID: 29690861
DOI: 10.1186/s12864-018-4681-2
call_split See protocol

[…] Biological pathways were identified using GOSeq software (v1.14.0) [] and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway annotations [] were used to identify biological pathways that were over-expressed among DEGs. GOSeq is an applic […]

library_books

Maser: one stop platform for NGS big data from analysis to visualization

2018
PMCID: 5905357
PMID: 29688385
DOI: 10.1093/database/bay027

[…] g Bowtie () to estimate the abundance of transcriptome using eXpress () and test DEGs with DEGseq (). In both pipelines, the resultant DEGs are subjected to a gene ontology (GO) enrichment test using GOseq () and visualization by REVIGO (). These pipelines finally produce an html report that summarizes the output of all the embedded tools ().The SAGE-seq category has a pipeline that is developed b […]

Citations

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GOseq institution(s)
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia

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