GO-Elite protocols

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GO-Elite specifications

Information


Unique identifier OMICS_26519
Name GO-Elite
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Version 1.2.5
Stability Beta
Source code URL https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/go-elite/GO-Elite_v.1.2.6_dev-Py.zip
Maintained Yes

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Documentation


Maintainer


  • person_outline Nathan Salomonis <>

Additional information


http://code.google.com/p/go-elite/wiki/Tutorials https://code.google.com/archive/p/go-elite/

Publication for GO-Elite

GO-Elite in pipelines

 (9)
2018
PMCID: 5780744
PMID: 29363429
DOI: 10.1186/s12864-017-4339-5

[…] levels among top 30% of all the transcripts were selected in each cell type., the functional enrichments of target genes of a tfbs and its corresponding transcription factor were examined using go-elite v1.2.5 with p-value threshold at 1, and after go-elite analyses a false discovery rate (fdr) test was performed with q-value threshold at 10−3 to correct for multiple comparisons […]

2016
PMCID: 5192059
PMID: 28050347
DOI: 10.1016/j.gdata.2016.12.006

[…] differentially bound) identified with high throughput experiments, an analysis was performed to identify, pathways, functions, and ontological categories that were significantly enriched. the go-elite function (within altanalyze) was used to perform enrichment analysis (adjusted p-value < 0.05) on numerous ontologies and annotation databases including geneontology, kegg, biomarkers, […]

2015
PMCID: 4344488
PMID: 25634895
DOI: 10.1093/nar/gku1377

[…] motifs (). found motifs were confirmed with an independent analysis in rsat (). for conservation analysis, ucsc genome browser dm3 phastcons15way table was used (). we conducted ontology analysis in go elite v1.2.6 (), and results were visualized in cytoscape v.3.0.2 (). for ldcv constituent analysis, we used data from gauthier et al. (), derived from a proteomic analysis of the corticotropes […]

2015
PMCID: 4429966
PMID: 25970274
DOI: 10.1371/journal.pone.0126783

[…] used for filtering reciprocal best hits. blast hits were processed to retrieve associated gene ontology (go) terms describing biological processes, molecular functions, and cellular components using go-elite []. bgi web gene ontology annotation plotting (wego) tool was used for plotting go terms []., expression levels of all the transcripts in the individual libraries (ctrl and ss) were assessed […]

2015
PMCID: 4433221
PMID: 25978040
DOI: 10.1371/journal.pone.0124823

[…] final analysis. the normalized raw counts per gene were used to identify genes that were differentially expressed (de) between breeds using edger. gene ontology (go) of de genes was performed using go-elite []. classification of functional processes of biological importance and of canonical pathways and networks of de genes were performed using ingenuity systems pathway analysis (ipa; ingenuity […]


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GO-Elite in publications

 (79)
PMCID: 5780744
PMID: 29363429
DOI: 10.1186/s12864-017-4339-5

[…] levels among top 30% of all the transcripts were selected in each cell type., the functional enrichments of target genes of a tfbs and its corresponding transcription factor were examined using go-elite v1.2.5 with p-value threshold at 1, and after go-elite analyses a false discovery rate (fdr) test was performed with q-value threshold at 10−3 to correct for multiple comparisons […]

PMCID: 5760858
PMID: 29191947
DOI: 10.15252/emmm.201708202

[…] fdr adjustment of p‐values corrected for multiple comparisons., to characterize differentially expressed proteins and co‐expressed proteins based on gene ontology annotation, we used go elite v1.2.5 as previously published (seyfried et al, ), with pruned output visualized using an in‐house r script (). cell‐type enrichment was also investigated as previously published (seyfried […]

PMCID: 5799810
PMID: 29086765
DOI: 10.1038/cr.2017.135

[…] institute, boston, ma, usa) and ranked by t-test statistics. for gene network and cdt analysis, expression levels were normalized with the rms method. the altanalyze pipeline was used to perform the go-elite analysis with 1.5-fold expression and 0.1 fischer exact test as threshold parameters. cdt visualization was composed using tableau 9.0 (tableau, seattle, wa, usa). mtrr ctd analysis and tph1 […]

PMCID: 5651906
PMID: 29057934
DOI: 10.1038/s41467-017-01168-1

[…] cntrl aso-treated nhdf are represented as a heat map in fig. . moreover, we analyzed molecular functions, biological processes, and cellular compartments of differentially expressed genes using the go-elite software. we found that extracellular matrix organization and cell proliferation pathways were downregulated in ptp4a1-silenced nhdf (supplementary fig. ). a subsequent pairwise comparison […]

PMCID: 5658700
PMID: 29038337
DOI: 10.15252/msb.20177754

[…] performed using r, and the name of the test is specified in main text., gene ontology (go) enrichment analysis was performed using go‐elite version 1.2.5 (gladstone institutes; http://genmapp.org/go_elite). pruned results (to decrease term redundancy) are reported. default parameters were used as filters: z‐score threshold more than 1.96, p‐value < 0.05, number of genes changed […]


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GO-Elite institution(s)
Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA, USA; Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands; Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA, USA; Departments of Medicine and Molecular and Cellular Pharmacology, University of California, San Francisco, CA, USA
GO-Elite funding source(s)
Supported by grants from the National Institutes of Health (GM080223, GM080223-06S1, HG003053) and the BioRange 1.2.4 research program of the Netherlands Bioinformatics Centre.

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