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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


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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 […]


Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome

PLoS Comput Biol
PMCID: 5825174
PMID: 29432412
DOI: 10.1371/journal.pcbi.1005989

[…] over-representation for each biological process go category with 5 to 100 genes available was quantified as an fdr-corrected p-value (across around 700 go categories) using version 3.0.2 of erminej software []. biological process go annotations [] were obtained from gemma [] (using downloaded on march 31, 2017). gene ontology terms and definitions […]


Mining DNA methylation alterations towards a classification of placental pathologies

Hum Mol Genet
PMCID: 5886226
PMID: 29092053
DOI: 10.1093/hmg/ddx391

[…] of etiologies and gas while some pathologies, such as chorioamnionitis, were excluded as controls in the validation cohort., these validated sites were not enriched for any gene ontology terms using erminej, with a 450k array specific background (). interestingly, 224/599 validated differentially methylated sites are found in enhancer regions. these sites include ones associated with genes known […]


Newborn genome wide DNA methylation in association with pregnancy anxiety reveals a potential role for GABBR1

Clin Epigenetics
PMCID: 5627482
PMID: 29026448
DOI: 10.1186/s13148-017-0408-5

[…] the top 500 uniquely annotated dmrs from dmrcate, we performed a pathway analysis. enrichment for gene ontology (go) classes was conducted using the over-representation analysis (ora) method in erminej with a minimum gene set of 5, and a maximum of 100 []., in order to verify the top dmrs from the dmrcate analysis, we used a second region-specific method: the python module comb-p []. comb-p […]


Cord blood hematopoietic cells from preterm infants display altered DNA methylation patterns

Clin Epigenetics
PMCID: 5397745
PMID: 28428831
DOI: 10.1186/s13148-017-0339-1

[…] statistically significant sites (“cell type-dm sites”) were limited to those with an fdr < 5% and a |δβ| > 0.20. cell-type dm sites were identified separately within the two birth groups. erminej was used to evaluate enrichment of gene ontology (go) terms in genes associated with the cell-type and prematurity-associated dm sites []., several other studies have performed similar […]


Asymmetric interactions between doublesex and tissue and sex specific target genes mediate sexual dimorphism in beetles

Nat Commun
PMCID: 5333360
PMID: 28239147
DOI: 10.1038/ncomms14593

[…] in functional categories representing gene product properties (for example, contributions to cell structure, their involvement in molecular pathways or their role in a biological process). we used erminej to test whether each functional category was enriched for differentially expressed genes relative to all other genes using gene score resampling (scores were based on adjusted p values) […]

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

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