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ErmineJ specifications


Unique identifier OMICS_04147
Name ErmineJ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for ErmineJ

ErmineJ citations


Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms

BMC Genomics
PMCID: 5824581
PMID: 29471790
DOI: 10.1186/s12864-018-4519-y

[…] with significant effects of time*treatment in both replicated experiments were examined for non-random distributions of function using a functional enrichment Gene Score Resampling (GSR) analysis in ErmineJ []. Briefly, GSR analysis examines the distribution of functions (given by the Gene Ontology (GO) annotation from Zhang et al. []) in the transcripts of interest, and compares that to what wou […]


Healthy Foundations Study: a randomised controlled trial to evaluate biological embedding of early life experiences

BMJ Open
PMCID: 5829768
PMID: 29374668
DOI: 10.1136/bmjopen-2017-018915

[…] Furthermore, resultant gene lists will also be interrogated for association with cellular processes, biological pathways and associated functions, using publicly available and validated tools such as ErmineJ. Collectively, this work will enable the identification of DNAm loci and regions associated with NFP status, and reveal whether epigenetic regulation of broader genomic functions underpins the […]


DNA methylation signature of human fetal alcohol spectrum disorder

PMCID: 4926300
PMID: 27358653
DOI: 10.1186/s13072-016-0074-4

[…] redundancy that may skew the results. As such, only 199 up-methylated genes and 190 down-methylated genes were analyzed for functional annotations using the overrepresentation analysis (ORA) tool in ErmineJ []. While no significant results were obtained using the gene ontology (GO) annotation with the list of down-methylated genes, the up-methylated gene list showed enrichment for genes associate […]


Lactobacillus rhamnosus CNCMI 4317 Modulates Fiaf/Angptl4 in Intestinal Epithelial Cells and Circulating Level in Mice

PLoS One
PMCID: 4595210
PMID: 26439630
DOI: 10.1371/journal.pone.0138880

[…] having high r2 values ().For physiological relevance, microarray data was also analysed at the level of gene sets that together encoded for particular differentially expressed functional GO terms by ErmineJ software (). Notably, this analysis revealed that the gene sets involved in immune system signalling pathways and regulation or lipid and carbohydrate metabolism GO terms were enriched by L. r […]


Ionotropic Glutamate Receptors Mediate Inducible Defense in the Water Flea Daphnia pulex

PLoS One
PMCID: 4370714
PMID: 25799112
DOI: 10.1371/journal.pone.0121324
call_split See protocol

[…] g Storey’s method []. Gene models, annotations and gene ontology (GO) terms were assigned to each probe according to the genome project data of D. pulex []. GO enrichment analysis was performed using ErmineJ overrepresentation analysis []. Among 21,987 genes bearing at least one GO term, GO subsets containing between 5 and 150 genes were included in the analysis. GO subsets with a Benjamini-Hochbe […]


Transcriptional Profiling of Hilar Nodes from Pigs after Experimental Infection with Actinobacillus Pleuropneumoniae

Int J Mol Sci
PMCID: 3876060
PMID: 24351863
DOI: 10.3390/ijms141223516

[…] ce (p < 0.05), overrepresentation of Gene ontology (GO) terms [,], and pathway in Kyoto Encyclopedia of Genes and Genomes (KEGG) DB [,] among both induced and repressed genes were conducted using the ErmineJ gene set analysis software [] and the Database for Annotation, Visualization and Integrated Discovery (DAVID) Online platform with a threshold of a minimum three genes annotated at each node. […]


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ErmineJ institution(s)
Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada

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