GoMiner protocols

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GoMiner specifications


Unique identifier OMICS_04138
Name GoMiner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for GoMiner

GoMiner in pipelines

PMCID: 5841087
PMID: 29545845
DOI: 10.3892/etm.2018.5833

[…] cell cycle and p53 signaling pathways in this study, and are listed in ., go enrichment results showed that a total of 50 terms containing upregulated and downregulated degs were obtained (). with gominer, clustering was carried out in public databases to discover some information associated with cell development and function. relying on gominer, we identified that the enrichment results […]

PMCID: 5841087
PMID: 29545845
DOI: 10.3892/etm.2018.5833

[…] to count go terms and kegg pathways () with a p-value of <0.01 and a gene number of >2. based on the standard clustering analysis method and novel gene clustering scheme, gominer (https://discover.nci.nih.gov) () was adopted to study the microarray data of sclc for the purposes of further evaluating the biological relevance, functional characteristics and false […]

PMCID: 4667476
PMID: 26627605
DOI: 10.1186/s12861-015-0097-2

[…] to ncbi/entrez databases. bowtie software was used to quantify the number of reads []. the raw counts were normalized using quantile normalization. normalized profiles were pairwise-compared using gominer software []. heat maps were generated using cimminer software []., histological samples were processed in the investigative histopathology laboratory at msu. immunostaining for p-h3 followed […]

PMCID: 4227137
PMID: 25005139
DOI: 10.1186/bcr3689

[…] average linkage hierarchical cluster analysis, and results were visualized using java treeview software []. ontology classification and pathway analyses were performed on the identified genes using gominer software []., the pbcs is a population-based case–control study conducted in two major cities in poland (warsaw and łódź) from 2000 to 2003 []. the pbcs patients were women ages 20 to 74 […]

PMCID: 3770002
PMID: 24066008
DOI: 10.1155/2013/160168

[…] significantly differentially expressed proteins were identified with a posterior probability of >0.95 by using the bayesian mixture model, and the spectral count difference was great than 10. gominer [, ] was used to find statistically represented gene ontology (go) biological processes (level 3) with log⁡10⁡(p) < −2 (i.e., p < 0.01)., cells were lysed in np-40 buffer (1.0% np-40, […]

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GoMiner in publications

PMCID: 5921988
PMID: 29699510
DOI: 10.1186/s12885-018-4354-1

[…] with flow cytometry and immunostaining. a msc-specific gene profile was screened by microarray assay and confirmed thereafter. gene ontology analysis of the selected genes was performed by gominer., tumor growth delay of murine mesothelioma ab12 cells was achieved after each cycle of cisplatin treatment, however, tumors grew back rapidly due to cancer cell repopulation between courses […]

PMCID: 5882305
PMID: 29662614
DOI: 10.18632/oncotarget.24633

[…] to five factors: prc, err1, gabp, creb and nrf1. two main groups associated the prc/err1 complex to either creb/nrf1 (686 genes) or to gabp (246 genes). the gene ontology database was queried using gominer software and p-values were computed for each go term based on the fisher’s exact test []. the main biological processes for different factor combinations were: oxphos and mitochondrial […]

PMCID: 5834518
PMID: 29500419
DOI: 10.1038/s41598-018-22292-y

[…] comparisons. for all sam analyses, the chosen delta threshold corresponded to the lowest median fdr (fdr = 0%)., gene ontology (go) enrichment analysis of the different clusters was performed using gominer. enrichment of go terms was determined using the 20,000 probe list as background. annotations with fdr < 0.05 were considered significant. go terms enriched in gene lists obtained […]

PMCID: 5801106
PMID: 29430376
DOI: 10.1007/s13205-018-1140-3

[…] or greater increases or decreases in fpkm values between the high-anthocyanin and non-anthocyanin accessions at the three time points described above. we conducted a go-enrichment analysis using gominer (national cancer institute, http://discover.nci.nih.gov/gominer/). blastp analysis was performed to find a tentative counterpart to the rice gene in the arabidopsis genome. false discovery […]

PMCID: 5841087
PMID: 29545845
DOI: 10.3892/etm.2018.5833

[…] and identified. gene ontology (go) function and pathway analysis of degs was performed through the david database. furthermore, microarray data was analyzed by using the clustering analysis tool gominer. protein-protein interaction (ppi) networks of degs were constructed using the string online database. protein expression was determined from the human protein atlas, and sclc gene expression […]

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GoMiner institution(s)
Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

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