GOstat protocols

GOstat specifications

Information


Unique identifier OMICS_04139
Name GOstat
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for GOstat

GOstat IN pipelines

 (5)
2016
PMCID: 4999207
PMID: 27560151
DOI: 10.1371/journal.pone.0161667

[…] and eliminated the influence of rna output size, sequencing depth and gene length. go enrichment analysis for the differentially expressed genes was carried out based on an algorithm presented by gostat [33], with the complete annotated gene set as the background. the p-value was approximated using the chi-square test. fisher’s exact test was used when any expected value of count was below 5. […]

2014
PMCID: 3921077
PMID: 24526835
DOI: 10.4137/GRSB.S13612

[…] format for running annotatepeakinbatch to get the nearby genes for each file. subsequently, we ran getenrichedgo from chippeakanno on each output-annotated file from annotatepeakinbatch to get the gostat for each file.22,26 we imported the output files containing nearby genes to the database and used sql language for the subsequent steps. we filtered each file to get nearby genes with distance […]

2014
PMCID: 4172843
PMID: 25347003
DOI: 10.1186/s12974-014-0163-x

[…] (=fold change ≤0.67) with an additional criterion being that the corresponding p values were ≤0.001., determination of statistically overrepresented gene ontology (go) terms was performed with the gostat analysis tool [36]. gostat was used with the following settings: go gene-association database and commonly used gene collections, affymetrix hg_u133_plus_2; minimal length of considered go […]

2014
PMCID: 4172843
PMID: 25347003
DOI: 10.1186/s12974-014-0163-x

[…] an additional criterion being that the corresponding p values were ≤0.001., determination of statistically overrepresented gene ontology (go) terms was performed with the gostat analysis tool [36]. gostat was used with the following settings: go gene-association database and commonly used gene collections, affymetrix hg_u133_plus_2; minimal length of considered go paths, 5; maximal p value […]

2012
PMCID: 3432130
PMID: 22952997
DOI: 10.1371/journal.pone.0044583

[…] categories using the david (database for annotation, visualization and integrated discovery) bioinformatic tool at nih, according to gene ontology biological process and molecular function terms. gostat from gene ontology was used to confirm annotations and validate gene groupings. go terms of similar biological or molecular processes were grouped together into categories under a label […]

GOstat institution(s)
Walter and Eliza Hall Institute of medical Research, Parkville, Vic, Australia

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