GOstat protocols

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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

 (25)
2017
PMCID: 5627237
PMID: 28978945
DOI: 10.1038/s41598-017-12978-0

[…] change (fc) ≥ 1 were set as the thresholds to identify the sdegs. fc is the ratio of fpkm between the two samples. go enrichment analysis of sdegs was carried out based on an algorithm provided by gostat, with the complete annotation results set as the background. the p-value was approximated using the chi-square test. fisher’s exact test was used when any expected value was below 5. […]

2017
PMCID: 5704797
PMID: 29145252
DOI: 10.1097/MD.0000000000008501

[…] genes expression levels are homogeneous without bias in each gene expression profile. then the threshold value of degs was set as |log fold change (fc)| > 1 and p value adjustment < 0.05., gostat is helpful to analyze biological processes (bp) of genes from high-throughput experiments, such as microarrays.[] go as the framework for the model of biology is used to describe gene […]

2016
PMCID: 5062329
PMID: 27563052
DOI: 10.1093/molbev/msw176

[…] as the ratio between the observed value and the mean of the control regions., we used chipseeker () to annotate dmrs to genes using hg19 knowgene table from ucsc. go analyses were performed using gostat rpackage () and using 13,455 human–chimpanzee orthologous genes (). gwas enrichment analyses were performed with traser package (). specifically, we considered 44,078 snp-trait associations […]

2016
PMCID: 5094087
PMID: 27809776
DOI: 10.1186/s12864-016-3212-2

[…] protein-coding genes located in target regions [] (extending 100 kb up- and downstream). all of these genes were classified into the categories of molecular function in the go database using the gostat program (p-value cutoff: 0.1, go-cluster cutoff: -1 and correct-method: benjamini) [] and were mapped to the kegg database using david bioinformatics resources [, ]., we used wafergen […]

2016
PMCID: 5159873
PMID: 27982037
DOI: 10.1038/srep34866

[…] sequencing project for c. farreri (unpublished). gene ontology (go) enrichment analyses for proteins from the scallop hepatopancreas were carried out based on the algorithm implemented in gostat, using the whole annotated c. farreri gene set as the background. go terms that were enriched within a given gene set were extracted with enrichpipeline. similar techniques were used […]


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GOstat in publications

 (243)
PMCID: 5896889
PMID: 29649209
DOI: 10.1371/journal.pgen.1007130

[…] (go) enrichment analyses were carried out for particular subsets of data that exhibited patterns of differential expression between white and green seedlings. to perform these analyses, we used gostat [] and go::termfinder [] implemented in the phytomine user interface (https://phytozome.jgi.doe.gov). for go term analyses, we used all annotated genes in the v2.0 im62 m. guttatus reference […]

PMCID: 5922378
PMID: 29721184
DOI: 10.18632/oncotarget.24897

[…] death or last follow-up., clustering was performed using a hierarchical clustering method using jmp built-in modules (sas institute inc., tokyo, japan). functional go annotation was performed using gostat [] and the database for annotation, visualization and integrated discovery (david) v6.8 []., statistical analyses were performed using r software [], bioconductor [], and jmp v10 (sas […]

PMCID: 5803922
PMID: 29415677
DOI: 10.1186/s12876-018-0752-8

[…] be significantly upregulated and downregulated., gene ontology analysis was performed using the database for annotation, visualization and integrated discovery (david) [] web service version 6.7 and gostat [] version 2.28.0 for bioconductor. similar results were obtained with both methods, but only the david results are shown in the article. the gene ontology annotations of significantly […]

PMCID: 5767605
PMID: 29375398
DOI: 10.3389/fphys.2017.01127

[…] model (bullard et al., ). degs were screened to identify those generating q-values ≤ 0.05 using the false discovery rate (fdr) method (noble, )., go enrichment analysis of degs was carried out using gostat (beißbarth and speed, ), with p-values approximated using chi-square tests, with all annotated genes used as the background. short time-series expression miner (stem, vision 1.3.11) was used […]

PMCID: 5742619
PMID: 29312322
DOI: 10.3389/fimmu.2017.01810

[…] for false discovery rate) to test statistical significant genes. only significant genes were displayed., the overrepresentation of specific go terms within the different clusters was analyzed using gostat with the goa_human database (minimum path length of 3 and benjamini correction for false discovery rate). all statistical significant genes per cluster were used as input, and all genes […]


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

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