GoMiner pipeline

GoMiner specifications

Information


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 citations

 (4)
2018
PMCID: 5841087

[…] and downregulated degs were obtained (fig. 2b). 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 were associated with cell division and cell cycle regulation. from the fig. 2c, it can be concluded that 80 genes were enriched in 167 go function […]

2015
PMCID: 4667476

[…] to ncbi/entrez databases. bowtie software was used to quantify the number of reads [69]. the raw counts were normalized using quantile normalization. normalized profiles were pairwise-compared using gominer software [70]. heat maps were generated using cimminer software [71]., histological samples were processed in the investigative histopathology laboratory at msu. immunostaining for p-h3 […]

2012
PMCID: 3436881

[…] moderated t-test from the linear models for microarray data (limma) package 3.4.3 [69] at a false discovery rate (fdr) of 0.01. gene ontology (go) analysis was performed using the high-throughput gominer [70] via the web interface using 1000 permutations, fdr<0.05, uniprotkb, ensembl, lmp and pdb homo sapiens databases and all evidence codes. clustering based on go category […]

2006
PMCID: 1693924

[…] of criteria including consistent regulation of different samples and replicates by = 2-fold as well as the magnitude of mean fold changes, their significance (one-samole t-test) and variation (sd)., gominer [48] was used to identify gene ontology (go) categories that were significantly (p ≤ 0.05) enriched in sets of both m-factor and p-factor regulated genes in relation to the frequency […]

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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