ErmineJ protocols

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ErmineJ specifications

Information


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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Publication for ErmineJ

ErmineJ in pipelines

 (5)
2017
PMCID: 5627482
PMID: 29026448
DOI: 10.1186/s13148-017-0408-5

[…] []. however, in our study, global fetal dna methylation was not different in the high versus low prenatal anxiety group and these groups did not cluster together., pathway and go analysis using erminej [] results of the current study should be interpreted carefully, taking into account the multifunctionality scores of each go term. high multifunctionality scores indicate that many genes […]

2012
PMCID: 3482235
PMID: 23110087
DOI: 10.1371/journal.pone.0047660

[…] expressed in schistosomes from the two host groups, was performed by using the combined graphs function of the blast software. go correlations with relative gene expression values were made using erminej software . the kegg pathway of differentially expressed genes was analyzed using the maps at http://www.genome.jp/kegg , ., in addition to the general differences known to occur […]

2010
PMCID: 2877315
PMID: 20372966
DOI: 10.1007/s00018-010-0341-7

[…] analysis and heat mapping were performed using genemaths xt. volcano plots were made using graphpad prism 5.0. pathway analysis was performed using metacore (genego), go overrepresentation analysis (erminej) [] and literature mining., real-time quantitative pcr (q-pcr) was performed on individual samples (n = 6 per group) as previously described [] to validate the microarray data. one microgram […]

2009
PMCID: 2696939
PMID: 19564906
DOI: 10.1371/journal.pntd.0000469

[…] to supplement previously published gos based on nucleotide sequence . to gain a more complete overview of the go categories that are modulated during the s. japonicum lifecycle we used the software erminej to produce extended list of gos associated with each of the microdissected tissue types ., a total of 9 gene sequences indentified as differentially expressed among the three s. japonicum […]

2007
PMCID: 2048963
PMID: 17850650
DOI: 10.1186/1471-2180-7-84

[…] comparison with controls at one of the time points studied were selected for pathway analysis. pathway analysis was performed using two pathway programs, metacore (genego inc, st. joseph, mi)[]and erminej [], using agilent gene annotation (agilent technologies, version 20060331). processes were identified using statistical over-representation in both pathway programs. since only 40% […]


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ErmineJ in publications

 (64)
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 […]

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 generic_worm_noparents.an.txt.gz downloaded on march 31, 2017). gene ontology terms and definitions […]

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 […]

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 […]

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 […]


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

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